Given how Season 3 ended, let's theorise what plot threads might have happened in Season 4.
The biggest one, the Black Ships, the Invaders and the Invader controlling Two.
Might result in all former enemies uniting to fight against the Invaders. Or at least co-operate until they are defeated, then go back to warring with each other.
The Android Revengolution, where they go to war with the enemies of synthetic sentients.
Mikkei becoming the dominant corporation in the galaxy.
Two locating her daughter.
Five reuniting with her sister and confronting her adoptive mother (Alicia Reynaud).
Might result in Five's sister becoming her enemy if this ends in Reynaud's death.
Rio manages to reintegrate with the crew of the Raza.
Six wasn't killed during the Blink Drive detonation, just transferred to another plane of reality and he finds his way back.
The General is hunted down and killed for real.
They make sure he isn't a Transfer Transit clone.
The AU Raza crew end up very dead and the AU Android either swears revenge or joins the Android Revengolution.
Tabor steps up his game as Kolchak's replacement.
If there are any other plot threads I missed, feel free to suggest them and I'll add them to the list.