Whilst cooped up in the container, Baird learns that Locust are capturing humans and torturing them. He gets a gun thrown at him and Delta heads off to find a Beast Barge where the prisoners are having gruesome things done to them. They find Tai Kelso, tortured to the point of being emotionally broken, and make the mistake of giving him a gun as he turns it on himself.
Sad, but, y'know. It could have been worse. It could have been Baird with meathooks stuck through his back.
The team head back to the Ilima sinkhole. Once there, a Raven comes to collect them, but they end up getting swallowed by the Riftworm. Miraculously, all the squad survive the fall and digesting (apart from Carmine, but who didn't see that coming?). They make their way to the hearts to kill the thing once and for all before it can sink anymore cities.
Sparing the gory details, the team cuts their way through membranes and arteries and destroys the worm's three hearts before sawing through it's skin to be washed out in a wave of blood. Covered in worm blood and mildly grossed out, Delta calls for a pick-up. What they get is a new mission. They head to the New Hope Research Facility which is supposed to hold information on the Locust stronghold; Nexus.
Baird and Cole are assigned with the important task of guarding the Centaur. Baird somehow manages to put a bomb-- extra-strength-- together in a couple of minutes with hardly any resources. After he's played his part, Dom and Marcus go back in to blow open the door whilst Baird and Cole wait out in the rain. Eventually the rain turns to razorhail, which ain't good for anyone's life expectancy, and they leg it out of there.
The squad battles up Mount Kadar in a tank, driving over icy lakes and making radical jumps, much to Baird's discomfort. Once they get underground, they run into a group of Stranded. Marcus has Cole and Baird escort the Stranded back up to the surface to be picked up by Ravens.
While Baird and Cole are busy; Locust were saw'd, Dom killed his wife and the beacon was set off, alerting COG forces to grindlift down into the Nexus, now they knew it's exact location. Delta Squad regroup and learn that the Locust are having a civil war between the regular Locust and the Lambent; Locust mutated by imulsion. The Lambent are attempting to take over Nexus and overthrow the Locust Queen, who plans to flood the Hollow after the Locust forces evacuate and genocide the remaining Lambent in the Hollow. In order to flood the Hollow, however, they must sink Jacinto, flooding the Hollow with the surrounding seawater. Delta Squad discovers these plans when Jack hacks into a Locust terminal and reveals several recordings from Adam Fenix explaining if they sink Jacinto, it would flood the Hollow with seawater, destroying the Locust once and for all.
Delta Squad then continuing fighting their way through Nexus and the Queen's palace, until they reach the throne room and confront the Locust Queen, who i surprisingly human-like. The Locust Queen explains that in order to prevent the humans from flooding the Hollow before the Locust escape, she has sent an army of Locust to assault Jacinto, distracting the COG army. When the Locust Queen escapes, Marcus orders Cole and Baird to track her down, leaving himself and Dom to battle Skorge in a series of chainsaw duels. Skorge too escapes on his Hydra after being overwhelmed by Marcus and Dom.
In order to reach Jacinto faster, Delta Squad hijacks two horsies Reavers and fly to Jacinto. In their journey back to the city, they are pursued by Locust driven Reavers and eventually by Skorge and his Hydra. Marcus manages to defeat both, however, causing the Hydra to be destroyed and Skorge to fall to his death.
Once at Jacinto, Delta Squad helps defend COG headquarters, with help from 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. Marcus and Dom go to fend off invading Locust while Baird and Cole stay behind to help assist with the Lightmass Bomb.
In the Jacinto sinkhole, Marcus and Dom manage to hijack a Brumak to speed up the operation. 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 then suddenly begins to mutate due to imulsion exposure and knocks the King Raven carrying the Lightmass Bomb into the imulsion, ruining the plan. 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.
The COG army and citizens flee from Jacinto on Ravens and boats as they all watch it sink underground. Much to Marcus, Dom and Baird's relief-- Cole and Anya make it out on another Raven.
Three hours after Jacinto was flooded, as the COG and Jacinto's remaining citizens are evacuated to Port Farrall, which becomes the home of the COG and Delta Squad for the next seven weeks. While there are sporadic Locust attacks on Port Farrall, it appears that the threat they posed to humanity has been all but eliminated. Seeking a more habitable location to rebuild humanity, Chairman Prescott chooses the island of Vectes; the island was a former COG naval base in the Pendulum Wars, could support a population of thousands, and is on the other side of a marine trench that is too deep for the Locust to tunnel under.
Delta Squad, along with Anya and Bernie, is dispatched to survey Vectes. To their surprise, they discover that the island, once called "Toxin Town" for the chemical weapons developed there and still technically quarantined, is pristine and inhabited by COG citizens. The town of Pelruan had been built to maintain the Vectes Naval Base, and its three thousand people have become self-sufficient after losing contact with the mainland following the Hammer of Dawn strikes.
Within two weeks, the COG moves the survivors of Jacinto to Vectes Naval Base and begins expanding the infrastructure. Prescott hopes to make the island into "New Jacinto," a place from which the rest of Sera could be repopulated. Everything is sunshiney happy. Apart from the vicious wild animals, violent Stranded and the small task of rebuilding humanity.