Eventually
but eventually you'll wind up fighting the enclave and being the hero once again.
Unless you'dd stay fateful to the enclave and be responsible for the deaths of all on the mainland.
Continuing where you left of:
Let's say you have this timer (like in Fo1) wich says '** days untill FEV release', once it hits 2O days your character looking at the Western horizon (FMV) notices a flash and a mushroom cloud (immediate ducks and covers) and at 0 days your character (at the end of the day) notices that there are no Toxic clouds drifting your way. After wandering around a little he finally establishes contact to some surviving enclave politicians (survived with the lawyers, rats and coacroaches) and you are told the be there agent on the land. Time jumps 6 months and you find you character arriving at a (new) bridge over a canion, with on the other side a beautiful city (New Arroyo, build with the Geck), with a mission... Kill the President, Kill the Chosen One.
Game starts, The first 30 days were meant somewhat like a tutorial.
You must have the option to change 'alignment' at any time, like in Fallout 1: you could work for some criminal and then turn him in. If you'dd turn yourself in you would become a Enclave infiltrant in Arroyo or vice versa or even have arroyo think you spy for them while you also spy for the enclave and give Arroyo false info or vice versa again.
But just one thing, An expansion like The Bad One would be aligned, wich is negative.