Act 3

Gordon is abruptly awakened by Bubby rolling his sleeping body down a ladder, to which the rest of the crew greets him. Dr. Coomer mentions that they have a good long while before they can reach the Lambda Lab, and the crew presses onward. They encounter their first of multiple alien sharks, and leap into the water to face off with each one, two of which Dr. Coomer beats to death with his bare fists. Bubby and Benrey are seen on multiple instances whispering to each other out of Gordon's earshot, in addition to Benrey becoming increasingly more antagonizing towards Gordon, though mostly in childish ways. An NPC mentions that Gordon's HEV suit is full of tracking devices, and Dr. Coomer follows up that he's been leading the military straight to them the entire time. Benrey mumbles with hostility that Gordon should die for doing so.

The crew reaches a hallway leading to the surface access gate, and before Gordon can enter through it, Benrey attempts to lead him into a side room through various means of persuasion, and Gordon hesitantly steps inside. The lights immediately go out and engulf the crew in darkness, and Bubby directs unseen soldiers to attack Gordon into submission, berating him for fucking up while Tommy protests in the background. Benrey revels in the sounds of the fight and of Gordon's pain, and promises that Gordon will be killed soon. Gordon's arm is heard to be sliced off as everyone seemingly becomes shocked, implying that it was not part of their ambush plans. Gordon is last seen being carried off by soldiers promising to murder him and dispose of his body, before Gordon falls unconscious.

Gordon later awakens to find he has been thrown next to a trash compactor, with his right forearm sliced off and bleeding profusely. He is forced to travel alone and mumbles to himself about being betrayed, soon finding Tommy alone in a separate room filled with green goo. Tommy insists that he had nothing to do with the betrayal, instead being tricked himself into staying out of it, and Tommy then joins Gordon's side to help find their way out together.

After swimming through a brief underpass, Gordon reaches a room on the other side filled entirely with a massive number of Dr. Coomer's clones, while Dr. Coomer himself announces that he's unleashed their power to attack Gordon with the desire to break free of his digital world and see the world inside the other man's head. "I've been outside, Dr. Freeman, there's nothing there. But YOU, I know theres a world in your dreams, AND I NEED TO GO THERE." Tommy manages to slaughter all of the clones on Gordon's behalf, all except for the real Dr. Coomer. One of the corpses reanimates as Dr. Coomer himself and announces a surprise attack, and appears to speak directly into Gordon's mind. "Every time you go to sleep, I can feel my body TORN apart... ATOM by ATOM... Its agonizing, Gordon... There's a world outside here, Gordon. AND I NEED YOU TO TAKE ME THERE..."

Dr. Coomer rejoins the two suddenly after his fit of existential dread, and cheerfully congratulates him on defeating all of his clones, seemingly avoiding responsibility for earlier. Having no other option, Gordon trusts Dr. Coomer and allows him to rejoin the duo, and Dr. Coomer explains that Bubby and Benrey have indeed been conspiring together about how to "handle a problem," in his words, the problem being Gordon himself. Its implied that they could either be angry at him for having trackers in his suit, or for other reasons, as passports are also mentioned. Gordon then announces that their next progression destination should be the Cybernetics Department for a potential replacement arm, which is on the way to the Lambda Lab, and they press onward.

Dr. Bubby is later found in one of the laboratories encased within a tube, which he announces is his tube from which they grew him in as a biological experiment, and demands to be let out, stating that they forced him back into it against his will. In a rather frantic tone, Bubby tells Gordon that he was lead on to falsely believe that Gordon was at fault for their struggles along the way, and that his betrayal was fueled by desperation. Once Bubby and Benrey had lead Gordon into the room where he was kidnapped, Bubby was then knocked over the head and imprisoned back in his test tube. Dr. Coomer, meanwhile, is repeatedly punching the glass tank. Gordon, after some convincing, turns his attention to Benrey being more of a suspect to betrayal than Bubby would be, and releases Bubby from his tube, allowing him to join the crew once more.

Gordon spots a skeleton sitting up on a light fixture and panics briefly as they quickly advance forward, discussing the incident with Coomer's clones from earlier, with Gordon remembering Dr. Coomer once stating that his power grows with every clone murdered. The skeleton seems to be following them and appears in a couple instances after that, until later, Benrey himself is found in a storage chamber speaking to another guard. The crew blasts both Benrey and the guard seemingly to death with their guns, though like usual, Benrey is found alive later in their path.

Confronting Benrey in a bit of a panicked state, Gordon watches in horror as Benrey pulls out an actual passport and demands to see his next, to which Dr. Coomer, Bubby, and Tommy all pull out their own, each with their names and faces on the front. Of course, Gordon has no passport to show off in return. Benrey then points out Gordon's lack of hand and taunts him for it, before Benrey joins and follows the crew as they move forward, likely without anyone's permission.

The G-Man is met formally for the first time by first calling out Gordon's name, allowing time to freeze and leave the two to confront each other in expositional conversation. The G-Man assures Gordon that the Resonance Cascade and the alien army will hardly hold as much weight compared to the rest of Gordon's fate, as he will be facing much more harrowing struggles in comparison, even going as far as to lightly taunt Gordon for not bringing his passport and thus making his own journey worse for himself by default. Nevertheless, the G-Man expresses interest in seeing Gordon succeed to the end, and assures that he and his "associates" will continue to support his journey, though their fate ultimately rests in his own hands still. Before departing, the G-Man also tells Gordon to ensure that no harm comes to his "progeny," whom has yet to be revealed at this point, but may imply itself to be Benrey. Gordon snaps back into real-time reality after the G-Man disappears.

The crew faces a series of encounters with the military outside as the venture onward towards the nearing Lambda Lab, with Benrey relentlessly shoving his passport in Gordon's face as well as teasing Gordon for his lack of a hand. Helicopters and planes are seen and heard flying overhead, and the crew is brought to a cliffside where one skeleton is spotted seated on one of the planes. The sound of helicopters grows increasingly more agonizing the closer they get along the cliffside, until when finally turning the corner, the crew encounters an all-powerful entity unlike they've ever seen.

The Helicopter Heap, a massive heap of active helicopters floating in one place, hovers nearby their cliffside and is unable to be destroyed by rocket launchers, seemingly regenerating new helicopters for each one lost. In the process of running from the Helicopter Heap, Gordon nearly plummets to his death off the cliffside, barely saved by Dr. Coomer's Extend-o Arms. The Helicopter Heap is eventually destroyed by an unseen force, and is never seen again. Also, Benrey kisses Gordon shortly after they escape the cliffs.

More encounters with the hostile military ensues as the crew (minus Gordon, due to his injuries) attack and defend themselves, with Dr. Coomer quite literally punching the top of a tank off with his own fists. They take refuge in a hole leading to a dark storage facility, with one skeleton to join them. Benrey and the skeleton show each other their individual passports in brief conversation, confirming the likelihood that Benrey and the skeletons are not the same entity. Act 3 ends after Benrey asks what happened to Gordon's arm for possibly the 4th time.

Trivia

 * The cast began planning plot points ahead of time starting with Act 3 in order to give a more coherent and satisfying story, including elements of foreshadowing and character development.
 * Wayne admits having experienced a genuine panic attack from method acting amidst the tense scenes.
 * The Coomer clones in the boss fight are combine soldiers and manhacks replaced with the scientist model.
 * The Helicopter Heap was a map loading error and was not planned, and could only be fixed by crossing a specific map trigger to delete the helicopters.
 * Benrey was seated on a rock in the radioactive sludge out of view while Gordon reunited with Tommy.