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This quest is available soon after The Waters of Life, and is obtained when you hear the Vault 101 Emergency Signal; you will notice the signal when you are near Megaton.
After re-entering the Vault, you'll have a small chat with Officer Gomez, who states that after you left, a problem occurred within the vault; in particular, some members wanted the vault to be opened permanently, and the overseer strongly disagreed with this.
When you return to the vault, characters that were kept alive from Escape! will remain; if they were killed, their bodies will be removed.
Talking to the Overseer
You can speak to the overseer to convince him to re-open the vault and allow. In doing so, you receive karma, and modified utility jumpsuit from Amata that increases your luck, repair skill and radiation resistance.
If you complete this option to get the vault open, you will occasionally see members scouting the wasteland in random encounters, if they are still alive.
Talking to the rebels
You can convince the rebels to stand down, and allow the vault to remain closed.
Assassinating the overseer
You can kill the overseer.
Assassinating the rebels
You can kill every rebel in the vault.
You can kill every person in the vault. When you do so, the Vault will be thrown into chaos.
Sabotaging the vault
You can sabotage the air filtration system within the vault in order to force everyone to leave. This requires a Science skill of 75.
Leaving the vault
This quest is optional, but you only have one chance at it. You can simply leave the vault for good and let them sort out the situation.