Act 1: Ashes - As the game opens 14 years after Emergence Day, a former soldier named Marcus Fenix is freed from the Jacinto Maximum Security Prison by his close friend, Dominic Santiago who needs Fenix's help in the fight against the Locust. Both managed to escape from the prison moments before it is destroyed by a Corpser and met up with the other members of Delta Squad, Anthony Carmine and Minh Young Kim. They received orders to find Alpha Squad and secure the possession of the "Resonator", a device intended to map the Locust underground tunnel network out for the Lightmass Bomb. En route to Alpha's last known location, Carmine is killed by a Locust sniper. Marcus, Dom and Kim are able to meet up with a Private from Alpha Squad, Augustus Cole who said that the rest of Alpha are at the Tomb of the Unknowns and their transmissions are blocked by the Seeders. Marcus eliminates the Seeders by using the Hammer of Dawn. After finding three more Privates from Alpha, Damon Baird, Gyules and an unknown Gear, they are ambushed by the Locust forces. Kim is separated from the others and is killed by General RAAM. While retreating into the Tomb, the unknown Gear is killed while providing cover fire. After Marcus defeats a Locust Berserker which kills Gyules, the team confirms with Headquarters that the Resonator is safe and are ordered to the Lethia Imulsion Facility, ten kilometers from their position. Marcus is also put in charge of Delta Squad in place of Kim.

Act 2: Nightfall - Dom suggests that the fastest way to reach the mine would be to borrow a Junker from a Stranded named Franklin who owes Dom a favor from the deals in the past. After reaching the camp, Franklin reluctantly agrees to give him the Junker on the condition that Cole and Baird should stay behind at the Stranded camp to help them defend against the Locust. Dom agrees and he and Marcus head across the ruined city as nightfall descends, bringing the Kryll out, the carnivorous bat-like creatures that attack anything in the dark. The two fight through the Locust forces to reach Aspho Gas Station where the Junker is kept and drive it back to the camp, defending themselves from the Kryll with an ultraviolet light equipped on the Junker that can kill the Kryll. The two arrive at the Stranded camp just in time to help defend it from a large Locust onslaught. Once the situation is secured, the team moves onward towards the mining facility in the Junker.

Act 3: Belly of the Beast - Delta Squad reaches the outskirts of the mining facility just as the Junker ceases to function. They make their way on foot through the abandoned facility and into the Imulsion mine tunnels, heading towards a pre-determined location where the effect of the Resonator should have maximum effect, all the while defending themselves against constant Locust onslaughts. The team eventually reach their target destination after Marcus defeats a Corpser and after securing the area, Baird setted the Resonator device off and they narrowly escape back to the surface. Unfortunately, the team quickly learns from HQ that the data collected from the Resonator blast was much too little to be of use for the Lightmass Bomb. However, a device found by Baird seems to already contain a near-complete map of the tunnel system with the data linking back to Marcus' father, Adam Fenix and his home, the East Barricade Academy.

Act 4: The Long Road Home - Delta Squad rides a King Raven helicopter to the East Barricade Academy, now ruined and heavily controlled by the Locust, losing a second King Raven to an attack by Nemacyst air spores in the sky. The team is dropped off just outside the Academy and are forced to fight their way through massive numbers of Locust on their way to the mansion where Adam Fenix lived. Baird discovers an APC in need of repair at the back of the manor and he and Cole rush off to repair it while Marcus and Dom search the manor for the data. After finding the hidden laboratory in the basement, they leave their cloaked robot, Jack to download the data and defend the house against the waves of Locust attackers. As Jack finishes downloading the tunnel maps, the two soldiers rush for the newly repaired APC behind the manor with a gargantuan reptilian-like Locust called a Brumak already charging towards them. Delta Squad and Jack reach the APC just as the Brumak smashes through the manor, escaping from the pursuing monster.

Act 5: Desperation - The team now rushes for the train station to get aboard the Tyro Pillar, an armored freight train carrying the Lightmass Bomb at the front. Along the way (Only in the PC version), they are held up by an open bridge with the busted controls thanks to the downed power lines. Using the fried corpse of the Brumak to connect the two transformers, they get the bridge down and make it to the station. The Locust attack them at the station and prevent Cole and Baird from jumping onto the train as it speeds past, leaving only Marcus and Dom to battle through to the front of the train as it travels across the wasteland towards the Locust stronghold. Unfortunately, they encounter General RAAM at the front of the train, guarding the Lightmass Bomb, though Marcus and Dom are able to defeat him. With a destroyed bridge quickly approaching as the train speeds ahead, Marcus uploads the tunnel data into the Lightmass Bomb and activates it, escaping from the train by jumping into a nearby King Raven with the help of Dom and Colonel Hoffman, seconds before the train falls off the tracks and into the Imulsion below. The bombs from the Lightmass launch into the Locust tunnels beneath, successfully eradicating most of an important Locust stronghold and almost all of the Kryll breeding grounds. Hoffman announces their victory to the rest of the world, but the haunting voice of the Locust Queen clearly says that the Locust have not been defeated and will continue to fight back.

Act 1: Tip of the Spear - The game begins with the Locust Queen providing a brief summary of what has happened in the Locust War over the last fifteen years, explaining how the war truly began, the Pendulum Wars, the Locust's survival of the Lightmass Bomb, and how Jacinto is now the last safe refuge for humanity. The story then moves to where Marcus, Dom, and Anya Stroud have gathered at Jacinto Med, a hospital in Jacinto. Ben Carmine arrives and becomes the rookie in Delta Squad. After a brief training session, Locust forces are spotted attacking the hospital and Carmine is ordered to stay behind by Marcus. During this attack, Marcus and Dom meet up with Tai Kaliso, a spiritual warrior that fought with Marcus in the Pendulum Wars. Together, Marcus, Dom and Tai move through the hospital, killing all of the Locust drones that entered and eventually meeting up with Carmine again. They force back the Locust forces outside of the hospital and into a full retreat. Anya then speaks with Dom about a lead she possibly had on his missing wife, Maria. Unfortunately, the lead was wrong, greatly upsetting Dom and resulting in him breaking a car window. After the assault on the hospital, Chairman Richard Prescott rallies the Gears, telling them of how the Locust Horde has survived the Lightmass Bomb and have returned stronger than ever, bringing with them a force that can sink entire cities. Soon, humanity will have nothing left to defend, leaving them one last option; an all-out attack on the Locust Horde in the Hollow. To do this, COG forces are to escort massive trucks called Assault Derricks towards the Locust occupied town of Landown and use Grindlifts to barrel down into the Hollow and fight back against the Locust. Upon arriving at the Derricks, Delta meets Dizzy Wallin, a conscript who drives Rig 314, also known as "Betty". On the way to Landown, Locust forces attempt to destroy the Derricks, only managing to destroy a small amount of them as the Gears fight back in defense. Once in Landown, the Derricks make their way to the cemetery while Gears on the surface provide protection in Landown and deploy the Gears underground. Unfortunately Locust forces attack once more, this time led by Skorge , leader of the Kantus. Dizzy confronts Skorge in order to prevent him from stopping Delta from heading underground. Tai somehow manages to leave his grindlift and also joins the battle. While the two battle Skorge, Marcus and Dom, unable to get out of the grindlift, look on helplessly before being projected underground into the inner Hollow.

Act 2: Denizens - Once underground, Marcus and Dom regroup with Carmine and move through the Hollow, supporting other Gears, such as Alpha Squad, who are under attack from Locust forces. As they journey deeper into the Hollow, they continue slaying Locust until Delta discovers the source of what is sinking entire cities; the Riftworm. Commanded by Skorge, the Riftworm sinks the entire city of Ilima before Delta's eyes, creating a massive sinkhole. The Locust are using the Riftworm to sink cities around Jacinto, punching holes around humanity's last safe haven in a desperate bid to eventually sink it. Delta quickly makes their way through the sunken city of Ilima, destroyed and in flames, battling through invading Locust and looking for survivors until they walk into an ambush. They fight back, but are outnumbered and nearly overwhelmed until Cole rescues them. Cole informs Delta that Baird and his jumpmate, Tanner, have gone missing. While searching for them, Delta comes across the remains of Tanner, which are barely recognizable. Seconds later, they find Baird locked up in a metal contraption. Baird says the Locust are apparently capturing humans and torturing them. Delta then comes across a Beast Barge, where the Locust take their prisoners to torture them. On the Beast Barge, Delta discovers Tai who has been severely tortured and broken emotionally. Marcus gives Tai a shotgun to fight with, but Tai, overwhelmed by the torture the Locust put him through, instead uses it to kill himself. Marcus and Carmine are both horrified. Marcus takes Tai's COG Tags and heads back to the Ilima sinkhole with the Squad. Once they're back in the sinkhole, Delta is picked up by a King Raven which arrives just before the Riftworm's sudden reappearance. Flying debris, caused by the Riftworm's tunneling, strikes the King Raven's tail, which causes it to temporarily lose control, Carmine to fall out of the Raven into the Riftworm's mouth, and the King Raven to be swallowed. Inside the Riftworm, Delta survives the "swallowing" and moves backward through the stomach and digestive system of the Riftworm towards the head. They find Carmine, dying after being burned by acid and partially devoured by Nemacytes, creatures that live inside the Riftworm. Carmine, with his dying breath, asks Marcus to tell his family he loves them and has Marcus send a letter to his brother, Clay, that he had written recently. Marcus then decides to kill the Riftworm before it can do more damage to humanity. Delta makes its way through the Riftworm, cutting open the worm's arteries to its three hearts. This ultimately kills the Riftworm and allows Delta to escape the massive creature by chainsawing through its flesh, emerging in a pool of blood.

Act 3: Gathering Storm - Delta Squad is then tasked with heading to the New Hope Research Facility which supposedly holds information on the location of the Locust stronghold, calledNexus, and the location of the Locust Queen. After blowing open the heavily armored door to the abandoned facility, Marcus and Dom maneuver through the still-active security systems until they reach the inner labs, learning that the facility had kept test subjects called Sires, which were mutated creatures resembling human and Locust mixed together. Accidentally awakening the hunchbacked monsters, Marcus and Dom kill most of the Sires and are forced to escape once they learned the location of the Locust stronghold and the Queen. They head off towards Mount Kadar, where there is back entrance to the Locust stronghold. After battling up Mount Kadar in a Centaur Tank, driving over lakes of ice, eliminating Locust outposts, killing a trio of Corpsers and a pair of Brumaks, Delta runs into a group of Stranded led by Chap, the owner of Aspho Gas Station from Gears 1. The Stranded had begun moving underground after their outposts were overrun by Locust forces. Marcus has Cole and Baird escort the Stranded back to the surface to be picked up by Ravens. Before leaving, Dom asks Chap if he had ever seen Maria before. Chap believes Maria was in a group that was captured by the Locust, and tells them to look for a waterfall near the Locust main highway. Marcus and Dom make their way towards Nexus, the Locust capital, by crossing a massive lake. During the crossing, they are attacked by Locust gunboats and a massive fish called the Leviathan, which is killed by Marcus when he hurls grenades down its throat.

Act 4: Hive - Once at Nexus, Dom convinces Marcus to help him search for Maria in the labor camps nearby instead of continuing with the mission into Nexus. After a small search and evading Locust patrols, they locate Maria, only to find her beaten, scarred, emaciated from starvation, and unable to stand or speak from endless torture from the Locust. Dom, not believing what has happened to her and extremely saddened, decides to euthanize her to put her out of her misery. He kills her, saying "I love you so much". Marcus encourages him to remember she is in a better place now. He also explains that he found a way to sneak into Nexus, though he tells Dom, "...if you wanna go in guns blazin', I don't blame you.", to which Dom replies "I wanna kill 'em all." Note: The "All Fronts Collection" included an extra chapter to Act 4; "Road to Ruin". It features Marcus and Dom disguised as Theron Guards, acting out Marcus' original plan to sneak into Nexus. As they fight their way through Nexus, Marcus and Dom activate JACK's beacon, signaling an accurate position for COG forces to drill down in Grindlifts and begin the assault on the Locust capital city. Reunited with Cole and Baird, Delta learns that the Locust are engaged in a Civil war against the Lambent; Locust who have been mutated from Imulsion exposure. The Lambent are attempting to take over Nexus and overthrow the Locust Queen, who plans to evacuate the regular Locust forces and wipe out the remaining Lambent in the Hollow. In order to accomplish this, however, they must sink Jacinto, flooding the Hollow with the surrounding seawater. Delta discovers these plans when JACK hacks into a Locust terminal and reveals several recordings from Adam Fenix explaining that, if they sink Jacinto, it would flood the Hollow with seawater, destroying the Locust once and for all. Delta continues fighting their way through Nexus and the Queen's palace, battling the most cunning and powerful forces the Locust have to offer, until they reach the throne room and confront the Locust Queen herself. The Locust Queen explains that, in order to prevent the Humans from flooding the Hollow before the Locust escape, she has sent an army to attack Jacinto, thereby distracting the COG Army. The Locust Queen briefly mentions Adam in a favorable manner to Marcus and Delta, but does not elaborate on how she knows him, brushing the subject off and ordering Skorge to attack them. When the Locust Queen tries to escape, Marcus orders Cole and Baird to pursue her, leaving himself and Dom to battle Skorge in a series of chainsaw duels. Eventually, Skorge escapes on his Hydra after being overwhelmed by the combined efforts of Marcus and Dom.

Act 5: Aftermath - In order to reach Jacinto as quickly as possible, Delta hijacks two Reavers to fly them to Jacinto. In their journey back to the city, they are pursued by Locust-driven Reavers and eventually Skorge on his Hydra. Delta Squad manages to defeat the Hydra, causing Skorge to fall to the ground below, killing him. Once at Jacinto, Delta helps defend COG headquarters, with help from Colonel Hoffman, from Locust forces and then is tasked with a new mission. The plan is to sink Jacinto using a Lightmass Bomb, ultimately flooding the Hollow. However, Seeder and Nemacyst infestation are a negative factor to the King Ravens that will bring the Lightmass Bomb to the position in the Hollow to set it off. Additionally, an opening must be made in order for the Ravens to get underground. Marcus and Dom head off to carry out the operation while Baird and Cole stay behind to assist with the Lightmass Bomb's preparation. In the Jacinto sinkhole, Marcus and Dom manage to hijack a Brumak to speed up the operation. With the Brumak, the duo blast through hundreds of Locust forces, including Reavers, Seeders, Nemacysts, a Corpser, and even a Beast Barge. Once the area is cleared of Locust forces and an opening is made, the King Ravens move in to deploy the Lightmass Bomb. The Brumak suddenly begins to mutate due to extended Imulsion exposure, and knocks the King Raven carrying the Lightmass Bomb into the Imulsion. Realizing the Brumak is going Lambent, Marcus, Dom, and Baird all use the Hammer of Dawn to make the Brumak explode, causing an explosion powerful enough to sink Jacinto and flood the Hollow, drowning both the Locust Horde and the Lambent. As the COG army moves away from Jacinto and watches it sink underground, Marcus attempts to contact Anya, growing distressed with the lack of response. Dom, solemnly holding his photo of Maria, comforts him, and the two soon see Cole, Prescott, Hoffman, and Anya on a nearby Raven.

In Gears of War 2, Marcus Fenix and the COG forces were forced to destroy the Jacinto plateau, the last major city on the planet Sera since the appearance of the Locust on Emergence Day 15 years prior, to flood the Locust tunnels and slow the spread of Lambent - Locust creatures mutated by their exposure to the volatile liquid known as Imulsion. In the eighteen months after the flooding of Jacinto, the human survivors have moved to the island of Vectes and have started to rebuild. After a generally quiet period, the Lambent began to emerge from underground. Hiding something, the COG head of state, Chairman Prescott, abandoned the COG. Now leaderless and being forced off the island, the COG disbands and separates to the safest places left. Victor Hoffman takes some survivors to Anvil Gate while Delta squad sets off on a Raven's Nest Class carrier, the CNV Sovereign, with the remaining humans to avoid further Lambent incursion. While Augustus Cole and his squad look for supplies from the ruins of his hometown, former Chairman Prescott arrives on the Sovereign, providing Marcus with a data disc that shows his father, the scientist Adam Fenix, is still alive. The ship is soon attacked by a Lambent Leviathan; Marcus and his team try to defend the ship, luring the creature into a trap set by Baird at a nearby bridge. Though the Leviathan is destroyed, the ship is also lost. Prescott is among the mortally wounded, but before dying, Prescott provides Marcus with an encrypted key with the location of a secret base known as Azura where Adam is being held. Leaving some of his Gears to help the survivors, Marcus, Cole, Dom, and Baird take off towards Anvil Gate, where they have the equipment to decode the key, while Anya and the rest care for the wounded.

The Gears are forced to travel across Locust-controlled bases, and the Locust Queen, Myrrah, alerts all her troops in their path to the Gears' approach. Marcus and his team eventually hijack a Locust gas barge to travel by air, stopping to help and rescue Dizzy, a skilled mechanic and driver. They arrive at Anvil Gate and help Hoffman defend against a Locust onslaught. Afterwards, they review the encrypted key to find the location of Azura but discover it is protected by a man-made Maelstorm, preventing arrival by air or on sea. Hoffman notes the location of a submarine in the ruins of Char, a nearby city, but they will need fuel. Dom suggests traveling to Mercy, where an Imulsion filling station is located, but also the home of his dead wife Maria. At Mercy, the Gears discover humans that have become Lambent from Imulsion poisoning, and fear the infection may spread. As they are surrounded by Lambent forces, Dom sacrifices himself by ramming a large truck into the tanker which explodes and allows the rest of Delta to leave for Char.

When they arrive in Char they come up against surviving humans that have come to resent the COG for what they did to their world. In an effort to gain the needed fuel for the submarine, Marcus and his squad run an "errand" for a former wealthy imulsion executive named Aaron Griffin. Dizzy is held hostage by Griffin and was only released when Marcus and his squad traveled to another tower in Char to find a lost cable car loaded with fuel. When they look back at the tower where Griffin is holding Dizzy, they see Queen Myrrah attacking and rush to help. After fighting through some of the Queen's guards, they rescue Dizzy, but lose the fuel. They then set off for the Endeavor Shipyards, where the submarine is located. After repairing and refueling it, they set off for Azura. After slipping under the Maelstorm, they find Azura is fashioned as a large resort. As they fight off the Locust that are also trying to get to Adam, and discover that Prescott had knowledge that Emergence Day was coming, as he had ordered the construction of Azura and brought the world's elite to it prior to the appearance of the Locust. Adam is able to contact the team via the security cameras on the island, and explains he has a cure to stop the Lambent but needs their help to execute it. Marcus and his team fight through the Locust to shut down the Maelstorm generator with Adam's instructions, allowing the remaining Gears and the Gorasni to arrive to provide air and ground support. As Lambent forces start appearing on the island, Marcus and his squad make their way to a hotel where Adam is being kept. En route, they face Myrrah, who reveals that Adam had been working with her for twenty years and refuses to let them help him complete his plan because it would result not only in the death of the Lambent, but the Locust as well. After dispatching Myrrah, the squad reaches Adam's room. After a brief reunion and hearing news about the death of Dom, Adam explains that Imulsion is a living organism, adapting itself to both Locust and human bodies to create the Lambent, and it is evolving quickly. Adam has developed an energy wave that, like a neutron bomb, will only destroy any cell infected by Imulsion. Adam had been in contact with Myrrah to try to stave off the effects on the Locust and to discover a cure that would not harm them, but could not find it in time.

Marcus and his squad escort Adam to the roof of the hotel where the energy generator for his cure sits. The Gears defend against Myrrah's attack as the machine powers up. Adam reveals that he will die shortly as well, having infused himself with Imulsion to study the lifecycle of immulsion and to test his cure. He tells Marcus to go live for him and then the machine begins to reach full power causing his cells to break down, killing him and leaving his son devastated. As Marcus agonizes over the loss of his father, Myrrah, still alive from the last attack, blames Marcus for what Adam failed to do. Marcus stabs and kills Myrrah with Dom's knife. As the machine gives off waves of its energy, the Lambent and Locust begin to die en masse all over the planet. As the Gears celebrate the end of the war, Marcus continues to mourn Dom and Adam's death, but Anya reminds him of his father's last words and that now, thanks to them, they have a tomorrow.

The observer then switches to another screen, watching the Outsiders JD, Del, Kait and Oscar Diaz. The four plan to raid a COG settlement, uninhabited and still in construction, in order to steal a fabricator for their village. Protecting the settlement are automated robots known as DeeBees. Fighting their way through the city, several coincidences on the part of the city's machinery help the team reach the city center, where they retrieve the fabricator. However, they are confronted by First Minister Jinn, transmitting via DeeBee, who angrily accuses them of taking her people. Before anything more can be said, the conversation is cut short by a rail car destroying Jinn's DeeBee. The team escapes the settlement and return to their village with the fabricator, but are quickly attacked by more of Jinn's robots. The DeeBees are repelled, but Reyna, village leader and Kait's mother, is furious at JD and Del for inciting Jinn. They attempt to explain what Jinn had said earlier, but to no avail.

At night, as JD and Del work to restore power, Kait notices strange creatures in the village. Chaos erupts as the creatures begin abducting villagers. Reyna barricades JD, Del, and Kait inside, then engages a humanoid creature in melee combat, managing to slice off its hand. Oscar tries to help, but the both of them are incapacitated. By the time the three emerge, everyone in the village is gone. Del likens the creatures' sheer numbers to a swarm. After JD finds the severed hand and cuts a crystal from it, Del suggests taking it to an expert: JD's estranged father, Marcus Fenix.

The three arrive at Marcus' estate and come face to face with the man himself. Marcus recognizes the crystal, but the tense reunion is cut short by the arrival of Jinn's DeeBees, who still seek to apprehend JD and Del. The four gear up and narrowly escape Jinn's forces, using a pair of old Mules to travel to Fort Reval. Marcus explains they need to get to the abandoned osmium mine on the other side of fort, where the COG dumped thousands of Locust bodies, which were completely covered in the same crystals that JD found, after the war. If the Swarm was related to the Locust in any way, they would find out there. The squad proceeds through the nearby town, discovering strange pods and bio-matter. Cutting a pod open, they discover the grisly remains of a COG soldier within, explaining Jinn's "disappearances" and leading the squad to realize that the Swarm is harvesting people. Soon after, Marcus is abducted by a Snatcher. The three chase after the Snatcher into Swarm territory, encountering new forms of the Swarm. They use an ore transporter to descend into the mine, where the Swarm have created a hive. They are attacked by a new creature, markedly different than the Drones they had encountered before, and covered in crystals. Pushing through heavy Swarm resistance, they find Marcus in a pod and free him. Marcus appears dead, but he manages to cough up the fluids in his lungs. He informs the team that while inside the pod, he was connected to the Swarm's network and could feel them, along with the disturbing revelation that the Locust had never died; they became the Scions, and are now using humans to build an army. Marcus then informs Kait that the Swarm is treating Reyna differently, and that she's being held at another burial site, located nearby at Tollen Dam.

The four then fight their way back to the surface. Marcus suggests taking a detour to get backup from a "friend", but Kait refuses to wait. The squad makes it to the top of the dam, but upon seeing the extent of the second Swarm hive, JD relents and asks if Marcus' friend can help. To contact him, they'll need to reach a radio tower, located in the nearby town of Speyer. They soon encounter a Scion Elite with a missing hand: the same one who took Reyna. The Scion speaks, saying Reyna is "right where she belongs". They kill the Scion and arrive at Speyer in the morning. Pushing through the town, Marcus gets in contact with his friend. Two giant mechs arrive at the agreed rendezvous point; their pilots dismount, revealing themselves to be Damon Baird and Augustus Cole. It's revealed that Baird was the one who was spying on JD and provided assistance in the COG settlement. Del, Marcus, Cole, and Baird board a King Raven, piloted by Samantha Byrne, leaving JD and Kait to pilot the mechs. The squad push through heavy Swarm resistance and return to the dam. After the mechs break through the dam and emerge on the dried riverbed where the hive is, a gargantuan Swarm creature erupts from the ground. The mechs and helicopter coordinate to take it down, but the Raven is downed. JD tears off the damaged helicopter's rotary system with the mech and uses it to kill the creature. The squad dismounts and enters the hive to find a partially-assimilated Reyna, who knows that if she's released, she'll die; nonetheless, she begs to be mercy killed. Everyone leaves the cave to give Kait some privacy as she bids her mother goodbye. Before she fulfills Reyna's last wish, Reyna tells Kait to take her medallion. Emerging from the cavern, Kait is consoled and holds up the medallion, saying that it belonged to her grandmother, who she never knew. On the back of the medallion is the sigil of the Locust Horde...

Following the events of the previous game, JD, Del, and Marcus are officially reinstated in the COG Army along with Kait, who is given the rank of corporal. Reformed as the new Delta Squad, they travel to the ruins of Azura at Damon Baird's request in order to launch a Hammer of Dawn satellite in an effort to restore the Hammer of Dawn network. After doing this, they return to the COG capital, New Ephyra, but Baird informs them that he still cannot locate the other satellites. First Minister Jinn finds out about the launch and orders them not to restore the network, since it would go against the wishes of the late Anya Stroud, who had decided to permanently decommission the Hammer of Dawn. Jinn receives word that Settlement 2 is under attack by the Swarm and sends JD's squad to assist the evacuation. Accompanying them in defending the settlement are Augustus Cole, Clayton Carmine, his niece Lizzie, and Fahz Chutani, JD and Del's former squadmate. It is revealed during the battle that JD, Del, and Fahz had previously been deployed in Settlement 2 to quell a riot which resulted in the death of civilians and prompted JD and Del to go AWOL. During a heated argument with Del, Fahz reveals that JD gave him the order to open fire on the civilians, causing Del and Kait to lose trust in JD. As the Swarm attacks intensify and threaten to destroy the evacuation convoy, JD orders Baird to fire the Hammer of Dawn prematurely. While the Swarm forces are annihilated, the Hammer of Dawn malfunctions and begins firing wildly. JD saves a group of civilians but is badly injured after failing to save Lizzie from being killed by the Hammer strikes.

Four months later, Kait and Del arrive at an Outsider village situated in the skeleton of the Riftworm to try convince them to join the COG. The village chief, Kait's uncle Oscar, refuses to join, but the village is suddenly attacked by the Swarm. During the battle, Kait is captured by a Snatcher and begins experiencing vivid visions of controlling the Swarm forces. She escapes the Snatcher, but is unable to prevent Oscar's death. COG reinforcements led by JD (who is now a captain) and Fahz then arrive to evacuate the village. Kait tells everybody about her visions, and Marcus recommends she head to a secret lab at New Hope to the north to find answers, with Del deciding to accompany her against JD's objections. As they reach the lab, Marcus explains that the chief scientist, Niles Samson, had been experimenting on the children of humans suffering from Imulsion poisoning. They find clues leading them to Mount Kadar, a former Locust stronghold.

Kait and Del continue on to Mount Kadar, where they find another secret COG lab hidden beneath the ice. There, they find Niles still alive as an AI construct and uncover the frozen remains of COG personnel and Locust. Niles explains to them that the Locust were the result of his secret genetic experiments, by manipulating the DNA of children infected with Imulsion and hybridizing them with the indigenous creatures of the Hollow. He also reveals that Queen Myrrah was originally a human who possessed a complete immunity to Imulsion and could control the Locust due to her genetics being used to create them. However, when her new-born daughter Reyna, Kait's dead mother, was spirited out of the lab by her father, Myrrah led the Locust to rebel against the scientists and gain their independence. Kait panics when she realizes she is the next queen, and demands that she be separated from the Swarm's hivemind. Niles puts Kait in a special brain scanning machine connected to a dormant Berserker called the Matriarch, which successfully severs Kait from the hivemind but also resurrects Reyna in the process as her consciousness still resides in the hivemind. Niles then flees, revealing that he has intentionally revived Reyna to let the Swarm finish what the Locust started. Niles is soon destroyed by the revived Matriarch and Kait and Del kill it before escaping the facility. Realizing Reyna is now the new Swarm queen, Kait reaffirms the COG's need to reactivate the Hammer of Dawn.

Sometime later, Baird takes the group to Vasgar, where the Union of Independent Republics' secret space program was located. Baird reunites with his former squadmate Garron Paduk, who is now the leader of a group of nomads surviving in the desert. Paduk reveals that the UIR had a rocket loaded with Hammer of Dawn satellites ready to launch, a fact both the COG and UIR kept secret from the public. He also reveals that the Swarm have recently become more organized and have developed new weapons and armor. Realizing that the Swarm's increased intelligence is the result of Reyna's resurrection, Kait, Del, and Baird resolve to reactivate the Hammer of Dawn as soon as possible. JD and Fahz also arrive to help Kait, with JD apologizing to Del and Kait for his previous deception. The squad manage to assemble and launch the rocket and acquire targeting beacons to help control the Hammer of Dawn, though they are soon confronted by a massive Swarm creature called the Kraken. The group barely manages to escape it when Paduk picks them up in a helicopter to fly them home. Upon returning to New Ephyra, the group makes plans to launch the Hammer of Dawn. Marcus theorizes that there is a central hive where the Queen resides to command and coordinate the entire Swarm force. This causes Jinn attempts to arrest Kait, intending to forcibly connect her to the hivemind to locate the central hive so the COG can destroy it to end the threat of the Swarm permanently. Before she can do this, however, the Swarm attacks New Ephyra. The Gears attempt to set up UIR targeting beacons to provide targeting data to the Hammer of Dawn, but the Kraken destroys them. Reyna, now transformed into the Swarm's queen, appears and attacks Kait, JD, and Del, forcing Kait to choose to save either JD or Del, leaving Reyna to kill the other. Kait and the survivor fight their way back to their friends but are attacked by the Kraken. The remaining soldiers fall back to New Ephyra's outer wall to fight off the Kraken and are soon overwhelmed until the squad's robotic companion, Jack, kills the Kraken by sacrificing itself as a targeting beacon for the Hammer of Dawn. In the aftermath, Marcus warns Kait that Reyna will return, with Kait remarking that they will find her first before discarding her mother's Locust necklace.