In the first hour of the season finale, Lexi tries to prove she's changed. Both Tom and Anne dismiss her and tell her to leave. Weaver convinces her parents that she's their best hope to get to the moon. They relent and Tom and Lexi head to the moon.
The ship's hull is damaged and Lexi put Tom in a cocoon to survive the lowered life support so they could make it. He wakes up in the ship back on Earth after Lexi completed the mission ... or so he thought. He eventually figures out it's not reality, but he's in a dream state. He believes Lexi's controlling him.
Instead, Lexi joined him in the cocoon and they are sharing a dream. She wants forgiveness. While he has regrets and wants to be able to forgive her. They come to an understanding after he realizes she's being genuine.
Together they wake up and see they are almost to the moon.