Well Suaside- that's up to you guys. What do you want to happen?
As I see it the group in Vault 15 are going to try to blow it up. Most of the slaves will die in the effort- either from the Strangers or in the blast.
Dwemer can't get the waterchip as that would ruin it for the future vault dweller. Or if he does get the waterchip, he loses it. I am thinking that as the blast goes up in the tunnels the overseers room collapses with it, destroying the site and Dwemer, Ivan and a few others are barely able to escape. Unfortunately, some of the strangers are out as well and will continue to cause problems.
As for you guys on top. If the Rovers attack the Vipers, the Rovers will probably win. But if Vault 15 goes up, then the Rovers will think their clients are gone as well, and they are out of a job. Either way Shady Sands has no future problems.
If you want the Vipers to live, they you will have to fight the Rovers in a pitch battle.
If the group tries to penetrate Vault 15, you will have to go through the human security as well as the strangers. As the strangers are powerful enough to tear a power armored BOS grunt apart, that might not be such a good move.
If I were the outside group I would fight it out alongside the Vipers, your allies, until the big bang to the East. The Rovers will dispatch and you may investigate, thereby reconnecting with the rest of the group.
The strangers will pop up from time to time. They also have an interest in the Mutants and will even have a hand in San Francisco- who do you think is really behind the space craft in FO2?