There's no good ending but only True Ending & Very Very Bad Ending only
You can reset the church story by going to your computer and type website *iamacheater* okay 👍
Viewing post in Church happy ending
after you achieve the ending called the happy ending. Shanice and Priest Bot defeat Pope Goku but end up coming back after getting kicked out due to Shanice calling the Bible mid and the Old Testament a prequel among other things. With the happy ending they can repair modules to near mint condition. The thing I pasted is from the official discord.
ending 2 (the happy ending) visit the church anytime. mention the place is rundown.. then visit again after 12 hours, from 17:00 to 20:59. ask about the pope. visit again the day after. choose to help. visit again the next day. tell FF to go to the vatican.
this ending is required to advance safely through some of the other storylines