From the description you gave, it sounds like you reached one of the “They know…” bad endings.
I cannot say exactly which Church ending you got without knowing every choice you made, but based on what you described, it seems that Shanice told you her thoughts about PriestBot, but she did not join you during Jun’s origin investigation.
If that’s the case, then you did not trigger the Church route that leads to the better outcome.
In the route that avoids this bad ending, Shanice will join you during Jun’s Origin Investigation.
To avoid the ending you encountered, there are a few important things that usually need to happen during the Church storyline:
- Reach the Church route where Shanice tells you her thoughts about PriestBot.
- Later, when you go for a walk alone, you will encounter PriestBot.
- When speaking with him, tell him the truth about what Shanice said instead of lying or avoiding the topic.
Following that path should prevent the “They know…” ending from triggering.
The rest of the events are better experienced naturally during gameplay. I won't tell you the rest.
Also, keep in mind that in the current version 0.90.16, the story is still incomplete.
The “Good” or more positive endings are planned for the upcoming major update 0.95.X, which will expand the later parts of the story.
More info about: 💀 All Bad Endings & ⛪ Church Endings (v0.90.16)