It definitely has some weird plot holes, but honestly... I think they may have done some of it on purpose. The game definitely doesn't take itself too seriously, so some of it may be a little tongue-in-cheek.
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You might be right about the tongue-in-cheek aspect. I also seem to remember that there is a way for Joanna to be the one to stay behind in the last part of the mission. You then have to hop on that hoverbike and head towards the hangar doors that the spacecraft left through.