She had complications after Emma's birth and so they had to take her to a hospital where she needed surgery and a few days to recover. Well the alliance is after them and stormed the facility, essentially, and Mal, Simon, and Zoe were there. Inara and River were yelling at them to come back to the ship so they could escape, and Mal was in with Zoe telling her he was not leaving her behind. She convinced him to go, because the alliance would have Emma if they took over the ship. So he left (it was really emotional, their scene) and went back to the ship with Simon. Inara was trying to tell Mal he'd done the right thing but he said that while he'd been through so much he'd always had her at his side and he felt so wrong and empty without her as his partner. So then River offered to be put under so she could search her brain for alliance secrets and then use the information as a sort of bribery to get Zoe back, which they didn't want to do since she was better and this might mess her up again, but she insisted. Then we see an alliance person telling Zoe that once she's well they will take her to a little known moon and drop her in a prison and forget about her, and no one would be able to find her no matter how hard they tried.