[Speculative spoilers ahead] I think season 2 will begin directly where it left off. June will get in the van only for it to be revealed that these particular officials are involved in the resistance/Mayday and this is an elaborate attempt to free her (this ties in with speculation Nick's a (#s "double agent") and his final words to her in season 1 (#s "just go with them...trust me")

Elizabeth Moss has spoken about season 2, saying (#s "it will be even darker/more disturbing"), so I think June's journey to freedom won't be without obstacles.

I feel like some weird love triangle will develop between Luke/June/Nick. If Nick is aligned with the resistance and helps free June than that could make her develop real feelings for him, especially now that she's carrying their child.

This would contrast to Luke's lack of involvement over the years (which is no fault of his own really), but could still have an impact on his relationship with June. Also, if Luke and June reunite and she has Nick's baby, that could create another curveball. Even though Luke is depicted as a relatively progressive/pro-feminist, he might struggle with the idea of raising 'another man's child'.

I have a strong feeling Luke's ex-wife will somehow be involved in the second season...I felt like her identity was purposefully omitted in the flashbacks, for all we know she might be an existing character.

Alexis has reportedly (#s "been bumped up as a main character next season, meaning Emily should feature more heavily"). Perhaps she escapes? Maybe she rejoins Mayday and helps free June? Or maybe they use her as a comatose human incubator?(ew).