How do you get to Ursula the Mutated, or to the Charon fight?

[Zarett]

I've completed the game twice with the same ending, going against the church, and I feel like I've missed out on a good part of the experience.

[Sir_Sam_Vimes]

Ursula: There's a well hidden spot you can drop down in the room with the bridge over a pit just after the giant laser robot in the Ancient Machine Works.

Charon: You have to complete Shirley and Delpha's questlines (possibly also Stone?) prior to defeating Loskid.

[Zarett]

Thanks for the reply. Would it be too much to ask if you could also help me with Shirley and Delpha's questlines?
The last time I saw Shirley was before the battle with Loskid, and with Delpha, I gave her all the soil samples and managed to get his memories back, but beyond getting him to change locations, I don't know what else to do.

[Powercrank]

you have to beat mutated Ursula. she gives you an item that you have to bring to Delpha after he moves to the arboretum and you've given him all the soil samples. Then later after you find Shirley near the end of the game and throw away her doll, you have to go back to Delpha and he gives you a flower that you have to bring to Shirley. You'll know you've finished Shirley's questline when she gives you a hug

Pretty sure you also have to have found the tree sanctum and finished the blader that carries a staff and teaches you spells quest (can't remember her name).

I'm not sure if helping Stone or bringing Assis(the doctors robot) his quest item are necessary but you may want to do their quests just in case.

Finally after you beat the normal last boss, you must decline the invitation in order to fight Charon.