Is there a way to stop the invasions without mods? I know that if you kill the Master and destroy Mariposa, the game ends, but if I do one or the other will that stop the invasion timer?

The invasion of what? The Hub? Necropolis? Boneyard?

This link should help you out ==> http://fallout.wikia.com/wiki/Fallout_endings

All invasions, I guess. Aren't they all linked?

I guess what I'm trying to say is, "Is there any way to stop the invasions without completing the game?". I ask because I want to be able to complete all the quests and explore at my own leisure.

In that case no. The longer you go without stopping the mutants the more things are destroyed.

So the only way is with mods that stop the invasions or allow playing after the endgame?

You should be able to do all of the quests if you don't take an obscene amount of time doing things. The only place I've had invaded was Necropolis. Other places do but only as a mention in ending slides.

I have a feeling that updates to the game made it so some places like the Hub don't get destroyed or the Boneyard so you can safely play the game for several game years. I am not even sure there is a time limit on the game anymore after you find the waterchip.

Edit: I would agree with Dustin81, Necropolis is the only one that gets destroyed in the game.

Necropolis doesn't even get destroyed if you don't go back to it and finish the game before the timer hits.

You can easily do every quest and finish the game normally without the mutants invading any location.

OK, thanks very much.