The only clue to their identities is a cargo bay full of weaponry and a destination: a remote mining colony that is about to become a war zone. With no funds for anything else, they decide to find a buyer for the weapons that they have. It's the future, looking the same all of the time is too vanilla. Traugott, allied with Mikkei, provides a white hole bomb to destroy the facility, but it is a trap: the bomb is a dud, and Two, Three and Six are captured. With her help, the crew fight their way to the shuttle, accompanied by Arax and two other prisoners, Devon and Nyx.
Meanwhile, Sarah tells Two she yearns for more social interaction than is available to her as an uploaded mind in the computer. Then as Galactic Authority ships intercept the Raza and soldiers storm the ship, the rest are knocked out with gas. She had a fatal, inoperable brain tumor, and the Android was made to house her mind, but Shaw decided against it. Five is able to foil the Ferrous Corp. Half the time it seemed like she was on the verge of tears, and that is just not appropriate for her character.
Usually when they permanently kill of characters in a show it's like a super long buildup; the character almost always lives if it's just shot at the end of an episode like that. Two believes that Ishida killed Nyx and wants revenge and the blink drive back. Six detonates the blink drive, apparently annihilating the shipyard and himself , but a giant spatial anomaly forms, and huge black spaceships come through it. Two kills the man sent outside the ship to make repairs and retakes the ship with help from Five, the rest of the crew being prisoners in the vault. The Mikkei second-in-command, who turns out to be a simulant herself, assassinates her commander and opens the anomaly to allow the aliens through.
Their memories wiped clean, they have no recollection of who they are or how they go on board. Chase hints that she and Two became romantically involved. Two, Three and Six recover the blink drive and use it to return to normal space, but Two refuses to use it again until they figure out what the Isida scientists have done to it. At his invitation, Three, Five, and Six's clones go to Zairon via travel transit to negotiate. Tash rejects Five's offer of a peaceful settlement and prepares to destroy the Raza with the stolen missiles, but the alternate Android shoots Tash and negotiates.
Ryo tells the delegates he will sponsor their membership in the League of Autonomous Planets to try to gain their support. Back aboard the Raza, someone disables the Android. The crew come to his aid, but are themselves captured, with the exception of Five. Facing death from her former friends, Five initiates a neural link of her own and uses Portia's most vulnerable memory against her in a mental struggle. When the Galactic Authority attacks the facility, Sarah's transfer is incomplete, so Shaw has to take her along when she flees. He sets an improved model, male this time, on Two. When Sarah awakes in her new body, Victor tells her they have a job for her.
When Three returns to the Raza, he brings along some sort of parasite that was implanted in him during torture; the crew find out in time and manage to eject it into space. Alex Rook created Two and wants her back. Ryo boards the station using a clone and orders the scientists aboard to activate the blink drive to take the now-defenseless station to Zairon, but since the scientists do not completely understand the device, the station ends up in a pocket of null space which is collapsing. When the local authorities find the Marauder, the crew use Brophy's blink drive to send Five back in time to earlier that day to arrange it so that they can return safely to the Raza, and back to the unaltered future using Brophy's blink drive. Two proposes destroying the shipyard by transferring the blink drive to the Marauder, taking it in close and overloading the drive. Jones Six is dead, Ryo Four is a ruthless emperor, and the crew now consists of Corso, Lin Two and Boone Three , who never lost their memories, along with Wexler and Tash from episode ten. The crew are ambushed by the Seers, who have predicted what they would do.
They return secretly and drop off the Android to infiltrate the facility and turn off the dampening field, before retrieving their crewmate. After experiencing hallucinations via their prior neural link with the ship, the crew wonder if they are linked to the Android's problem. They find valuables, a stasis pod carrying Sarah, a woman from Three's past who is dying from an incurable disease, and an entertainment android named Wendy. They find that Tabor's girlfriend Ambrosia is being held hostage by Goren, a business rival. Although she learns more about Four's past, as well as her own before she boarded the ship, she becomes stuck in her dream-like state. Later, a delegate is murdered. Dark Matter has been cancelled, follow for the Twitter fan campaign.
And as a bonus they could introduce any new actor. Two and Three impersonate their captured counterparts to infiltrate the other ship and steal their blink drive. Six volunteers to enter her visions in order to rescue her, and discovers more about his own past. Two captures Corso and executes him. With the link broken, they return to their normal amnesiac selves. As Four attempts to convince Akita of his innocence, the crew eventually decide to go after him and arrive in time to save him and Akita from bandits. Later, Portia proposes an alliance with Ferrous Corp's Commander Nieman against a common enemy.
Later, Commander Nieman and the alternate Portia and Boone contact Ryo about an alliance. I thought this was because of the odd separation of the two episodes. Ryo sends mercenaries to take back the blink drive and kill his former friends. The first episode ended with Five secretly putting on the mind probe in her room and seeing Sarah. The missiles and most of the money are returned and all prisoners exchanged.
During the course of the series, 39 episodes of Dark Matter aired over three seasons. So it wasn't much of a choice - 100% chance of losing the war drive on Zairon or a less than 100% chance of losing drive on station. The Android then extracts information from the ship's corrupted data files that states that all of them, with the exception of Five, are wanted murderers and thieves. After regrouping, the crew rescue Four. Then those things were not mentioned for the rest of the season 12 episodes. Teku sets Two free for her help in Ryo's escape. After an explosion kills the rebel leader, Six negotiates with the Traugott security detachment, convincing them to negotiate rather than fight, but one colonist treacherously shoots the detachment's leader, reigniting the fighting.