Red Matter Ending Explained / Story Explained

Since I haven't seen it too many other places on the internet, here is the whole Red Matter story as I understand it, with some artistic license. Hopefully I got it mostly right. And SPOILERS!!!

Sasha (the quantum physicist), Nikolai (the security officer and head of the base), Olga (the communications officer), Irina (the biologist), and Stas (the engineer) were all on the Volgravian base on Rhea, conducting scientific research. Sasha discovered teleportation and Nikolai was very interested in that technology. Meanwhile, Irina discovered a red mold that was indigenous to the planet, and saw that it was dangerous and spreading uncontrollably.

She reported it to Nikolai, but he ignored the danger in favor of prioritizing Sasha's teleportation research. Irina and Stas were a couple, and she shared her concerns with him about the red mold. Stas, being more of a free spirit as evidenced by his failed loyalty tests, encouraged Irina to do something about it and to not trust Nikolai.

So Irina tried to send a secret message out to Volgravia: "We're all in danger from this mold, we need to pull out ASAP, but our security officer won't do anything about it". But Olga, being the communications officer, discovered the secret message. She and Nikolai were in love, and Olga wanted to climb the Volgravian ranks, as evidenced by the trophies and photos of other accolades in her room. So she snitched to Nikolai.

Nikolai retaliated by injecting Irina with a syringe of the toxic red mold, killing her. Olga felt conflicted. She had thought she was doing the right thing, but now it was her fault Irina was dead. Stas mourned Irina and got angrier and angrier—and more and more alcoholic—until he confronted Nikolai with a weapon in the reactor room. Nikolai shot and killed him.

Meanwhile, the red mold was still spreading uncontrollably, and Nikolai finally recognized the danger it posed. He sent a secret message to Olga, telling her to meet him at the escape pods ASAP. They got off the moon and callously left Sasha behind to succumb to the red mold.

Nikolai and Olga hatched a plan to get the teleportation research that had been left behind on Rhea. (Whether they joined up with the Atlantic Union or acted as independent agents, I don't know.) They went back to the base and found Sasha's body. His brain was still active, maybe the red mold had put him in a comatose state. Somehow they figured out a way to put Sasha and Nikolai's consciousness into a simulation together, so Nikolai could direct Sasha to retrieve the research.

In the simulation, they tell Sasha that he's an Atlantic Union agent, code name Epsilon (Epsilon translates to "5th letter," maybe referring to Sasha being the so-far-unaccounted-for 5th member of the team), sent on a mission to Rhea to find out why the base was abandoned and retrieve whatever classified information the Volgravians have left behind. It's implied there is a Cold War situation between the Atlantic Union and Volgravia. Epsilon—Sasha—is you. The professor whose voice is guiding you is really Nikolai putting on an Atlantic Union accent.

As you progress through the simulation, your mind is trying to wake you up to the truth, manifesting both as a mysterious figure in an astronaut suit and as a red pawn moving through a chess game (chess was one of Sasha's hobbies). Whenever you enter spaces covered with the red mold, you get a rare moment away from the professor's monitoring, so your mind has also left cryptic messages there.

When you finally teleport into the research room, you catch a glimpse of Nikolai running the simulation. With the research in hand, as you get closer and closer to beaming it up via satellite, your mind fights harder and harder. You see messages more plainly, warning you to "keep the secret" and "don't trust him". You hear a female nurse's voice talking to the professor about the simulation, warning him that the subject is fighting against the simulation, but the professor isn't willing to shut it down when he's so close to getting the research this time. He also lets it slip that he knows Sasha.

At the climax, your mind manifests a chess game in which you play the last few moves to checkmate the red king. Your mind has beat the professor's. You wake up in the simulation room looking at your own body. Behind you is the nurse's silhouette. She says that Sasha did not survive the simulation. But here you are. Somehow since Nikolai was connected to you in the simulation, your consciousness has taken over his body. But the nurse doesn't realize it. Just before the game fades to black, she says in a Volgravian accent "Slava, comrade." Or translated, "Glory, comrade." She is Olga.

(Maybe we'll get a Red Matter #2 in which we fight against Olga? Doubtful, but could be fun.)

[edit: check out the comments, there is an alternate and possibly more correct theory where the professor really is from the Atlantic Union and the nurse is a Volgravian operative trying to free you.]