Somehow they winded up in a ghost town because a solar flare made their GPS useless. Faith promised to let Frank lead without interfering even if everything went wrong. Fojan wasn't even paying attention to the misson briefing and isn't sure when things even went wrong.
After Francis ran away Edan hoped Faith might escape too, faiths known the truth about the clones for a while. Edan even bribed a doctor to sneak in some dna from a mystery man so faith would be healthier than the other clones when she was conceived. Faith just wants to try harder to prove her loyalty.
Fojan was the only one to go looking for Francis. They were shocked francis didnt die yet. Francis way angry at first and didn't trust him but it felt good to talk to someone who knows about all the nasty side effects. Of course everything went wrong and Francis had to go even deeper into hiding but the two play online co op games together in secret after.
Frank and Faith contined competing for missons, presentations, everything they could. Faith often upstanding Frank because even after learning the truth he remained in denial about how bad his health is and how replaceable he is. Both were put under stricter observation after Francis left, and there constant competition for the spot light is what allowed Fojan the freedom to reconnect with Francis in the first place.