Season 2 finale was
so many potential plotlines
Yeah, they set things up nicely with the Freelancers having captured Liber8 and Kira and having them locked up. You have Alec in some alternate timeline trying to save that girl, which I agree with @StanJones that they didn't really set up his motivation greatly why he made the decision he did. He was down for helping Kira throughout the episode then seemed to switch his mind towards the end.
Carlos on his F' the Police steez now that the bald head chief has gone corrupt and is in Eiser's pocket. Speaking of Eiser I did not see him being Alec's father, even if he is telling the truth. James being future Alec's son was a dope twist I didn't see coming either.
Overall season 2 was a nice improvement in quality over season 1 and started to pick up as it progressed. Glad I stuck with it because I was close to dropping the show. It still needs work in some areas in explaining the exact motives of Liber8 and Alec, but there is enough good stuff there to make it a solid sci fi show.