Jun doesn't actually leave; she gets kidnapped.
What you're encountering is one of the "They know…" bad ending variants.
There are two slightly different versions of this ending depending on your progress in the story:
- One happens if you have never met BigDaddyHurt.
- Another happens if you have already met BigDaddyHurt.
How to prevent this bad ending:
To avoid this outcome, you need to make sure PriestBot joins the Origin mission.
The general steps are:
- Get the Church's Good Ending.
- Continue progressing through the story.
- Listen to Shanice's thoughts about PriestBot.
- When you encounter PriestBot, do not lie to him or avoid telling him the truth.
- If everything is done correctly, PriestBot will join the Origin mission.
Why does this bad ending happen?
At the burnt lab, there are several hidden surveillance cameras that someone is using to monitor the area.
- Jun cannot detect the low-frequency signals coming from those cameras.
- Because of that, no one notices them during the mission.
- PriestBot, however, is able to detect those signals and certain military technologies.
If PriestBot does not join the mission, the cameras remain active, which allows whoever is monitoring them to intervene, leading to Jun being kidnapped and triggering the bad ending.
The exact reason PriestBot refuses to join when you lie to him isn't fully explained.
It may be related to trust issues, or possibly something happening between Shanice and PriestBot behind the scenes.