The second best thing was Peter's treachery. Not that I liked it - I think I'm still routing for the good guys - but it was a sound plot development. I never liked that guy, and it was consistent with naivety of Alan and his group that they would put so much trust in Peter. Or maybe it was an understandable lack of understanding, not naivety, but it amounts to the same thing.
Also good was the destruction of the base, leaving us not knowing whether Sarah survived, especially significant because she's presumably carrying Alan's baby. And Julia apparently in charge of Ilaria, or pretty high up in its command, was also a good move. It brings home the point, already made by Peter, that no one with those eyes can be trusted.
So Helix has some pretty intriguing pieces in place for its second season, including the canister that Alan rescued, which I have to hope was the cure.
But I gotta say that I hope Helix plays them better than it did in the first season, which was slow moving and confusing throughout much of its run. The last two episodes finally got the narrative up to speed, but the unanswered question of who the Ilarians are still looms large. Let's hope that whatever their identity, we don't need all of the second season to discover it.