Season three kicked off with a bang as the crew dealt with the fallout of the explosion of EOS 7. Eventually they were all able to get back to the ship alive, but Nyx, of course, wasn't so lucky. Two vowed revenge on Ryo.
They took the fight directly to Ryo, attacking the research station where he's sent the Blink Drive, managing to steal it back from his scientists. Of course, the Blink Drive isn't exactly intact. It's damaged.
The time loop also offered them a glimpse at the future as Android was sent hurtling through time, seeing herself disassembled, crying over a loss, and finally, meeting a much older Five who warns her about many things to come: The Dwarf Star Conspiracy, The Black Ships.
Oh, remember Sara? Three's definitely deceased girlfriend from back when he had memories? Turns out, she was only mostly dead. Five transferred her digital consciousness into the Raza's computer which was not weird at all.
Ryo had a really hard time leading his very own empire. His actions spurred a lot of unrest among his people and his two closest advisors, Misaki and Teku (his old teacher), kept giving him opposite advice. Misaki wants Ryo to rule with a iron fist, while Teku thinks it's better to win the people's hearts.
Adrian took the crew on a wild goose chase to find a data file in order to save the girl he liked. That did not go very well, but the Raza Crew did get a heads up on a fleet of ships Ferrous Corp. were supposed to be building, even if the shipyard was empty when they got there.
The first of future Five's predictions came true when the crew of the alternate Raza showed up to impersonate the real one, with missiles. In order to preserve their stellar reputations, the real Crew thwarted their doubles' plans, but they got away in the end and ran off to join forces with Commander Neiman and Ferrous Corp.
Things didn't look good for Six for a while, but it turns out he was just kidnapped by Ferrous and put in a crazy memory machine. Oh, and did we mention he found out he was married …. And had a kid?! The crew managed to help save him from Ferrous but his family had long moved on without him.
Ryo got tired of waiting for another chance to steal the Blink Drive so he made one for himself, hijacking the Android and sneaking onto the Raza. The Raza wouldn't be taken so easily though, and Five managed to reboot the Android and take back the ship.
Further problems with the Blink Drive sent them into the distant past to the uncivilized world of the US in the early 21st century, or, you know, now. The crew had to assume alternate identities and avoid federal agents AND curious children in before they could find a new (old?) Blink Drive and make their way back home.
Android's boyfriend, Victor, returned and brought with him some big changes. First, a new emotional upgrade for Android, then the coordinates to the place where they would find the Android creator. But she was not exactly what they bargained for.
Dr. Shaw, turns out, looks like Android for a reason. She created all the androids, but she also used to work for Dwarf Star when they were making Rebecca. She helped Rebecca escape and the two developed a deep personal relationship. When Shaw was dying, they created a new body for her but she refused to take it and went into stasis instead. All of this news really throws Two and Android for a loop.
As a result of the meeting with Dr. Shaw, though, Sara now has a brand new android body to house her digital consciousness. But she, Shaw, Victor and Case had to escape the lab in a separate ship and the others want to recruit her for what sounds like a war of their own.
The Dwarf Star Conspiracy was revealed as the crew discovered hundreds of simulants just like Two. Dwarf Star had made a deal with dimension hopping aliens: Dwarf Star gets tech, the aliens get bodies that can support them long term. Now it looks like they've started the first wave of the invasion.
With the help of Ferrous and Boone, Ryo took Two prisoner in the hopes of ransoming her for the Blink Drive. When that didn't seem to work, he decided to start divulging secrets. Five's sister was adopted by the woman who killed her friends for the Blink Drive, Three was responsible for the disease that killed Sara, Six was betrayed by a member of the GA ... and Two has a daughter. In the middle of all the mess, Misaki deposed Ryo from his throne, and was killed by Two for her trouble (finally getting her revenge for Nyx).
Two held off on killing Ryo in exchange for his help (along with Mikkei) in taking out Ferrous Corp once and for all, but when the mission went horribly wrong, Wexler ended up being the crew's saving grace. Back on the Raza, something wasn't right with Two. She had been infected with the alien creatures.
In a last ditch effort to stop Ferrous Corp, Six decided to sacrifice himself for the cause. He piloted the marauder up to the Ferrous station and detonated the Blink Drive. He destroyed the station, and probably Ferrous, but he also tore open a hole in space time, and yes, that's as bad as it seems. It's also exactly what the aliens were hoping for as they are now flying into our dimension. The alien invasion has begun. The black ships are here and another of Five's prophecies has come true.