Tower Level 1: the main floor of the Cathedral.I shall give you two options for doing that when the time comes, a brute force approach and a sympathetic ear approach. Your main goal here is of course to get rid of the Master, found at Lair Level 3 (or the 3rd level of the Vault). Enter the first area, and click on the entrance grid to the door to be teleported inside. If for some fluke of nature the Cathedral isn't yet on your World Map, it is due south of the Bonyard two grid squares, right along the coast. Since the Master and the Cathedral is perhaps a more dramatic ending, it is why you've found it at the end, though it isn't any more difficult than the Base and actually can be quite a bit easier depending on how you approach it. It can be done before or after the Military Base, it makes no difference since you have two main quests really form one goal: to end the mutant threats.
The Cathedral is one of your final objectives of the game.
When you're ready for the assault on the Military Base, keep in mind you can ask a few paladins from the Brotherhood to assist for extra (hehe) support.
