Prerequisites: Join the Unity (reveal the location of Vault 13 to the Lieutenant or the Master), 500 days pass while the latter is alive (or 13 years regardless).
It is done. Vault Thirteen belongs to the Unity and the Master. Your knowledge of the Vault defenses saved many mutant lives during the attack. You personally made the final kill when you took the life of the Overseer. You will certainly become one of the finest soldiers for the Unity, and your skills will see you rewarded often in the future. You are happy. But there remains the tiniest doubt of what could have been...
The death of the Master was the first major step towards ending his mad dream of conquest and enforced peace, but it is the destruction of the Vats that neutralizes the mutant threat. Without the ability to create more mutants and enforce their harsh brand of justice, the mutant armies flee to the east, beyond the no-man's land.
Prerequisites: Destroy the Military Base before taking the Cathedral.
You managed to destroy the Vats, then you killed the Master before he could realize his twisted plans. With the Master gone, his armies flee to the east in fear of retribution from the remaining normals.
Prerequisites: Tandi is dead or not rescued, Aradesh is alive.
Aradesh grieves for his slain daughter, Tandi, but eventually builds Shady Sands into a respected community which is prosperous for many years, before his untimely death at the hands of a Desert Raider.
Prerequisites: Both Aradesh and Tandi are dead (or the latter not saved from the Khans).
With Aradesh dead, and Tandi missing or killed, Shady Sands needs a new leader. After several elections, they find they cannot be governed by a single person and create a guiding council. Shortly afterwards, the Raiders regroup and attack Shady Sands, burning the small community to the ground.
In the original write-up of Junktown, the "ending sequence" was reversed from its final incarnation. See the alternate endings for the original versions, which were changed because the marketing department decided at the last minute that the game had to "reward good and punish bad".
With Gizmo out of the way, Killian enforces his brand of frontier justice on Junktown. The city remains orderly but small, as travelers steer away from his rigid sensibilities.
[With the background picture being a gallows behind Killian with shadows of dead men hanging from it.]
Gizmo takes control
Prerequisites: Gizmo is alive.
Junktown becomes the new boomtown under the careful, and profitable, guidance of Don Gizmo. He profits the most, and continues to increase the size of his casino, and the scope of his power, until he chokes to death while eating some iguana-on-a-stick.
Under Gizmo's leadership, Junktown becomes a trading center and resort, where people come from miles around to gamble, spend money and enjoy themselves in relative safety. Gizmo keeps the town prosperous but healthy, as he has no desire to injure his own affluence. The inhabitants of the town become wealthy and famous.
[With the background picture showing Junktown as a Reno-like casino with electricity and clean streets free of any drug dealers or riff-raff who might endanger Gizmo's operations.]
Destroyed by mutants cut
Prerequisites: The Master is still alive within 210 days.
The mutants are slowed, but not stopped, by the brave defenders of Junktown. When the army finishes their brutal siege, nothing of Junktown remains.
The Brotherhood of Steel helps the other human outposts drive the mutant armies away with minimal loss of life, on both sides of the conflict. The advanced technology of the Brotherhood is slowly reintroduced into New California, with little disruption or chaos. The Brotherhood wisely remains out of the power structure, and becomes a major research and development house.
The Brotherhood of Steel, under new leadership after the death of Rhombus, becomes an overzealous, techno-religious dictatorship. In 20 years, the Steel Plague devastates the newly formed New California Republic, and starts a Dark Age that could last a thousand years.
Prerequisites: Kedrick is alive, or the Master is alive for 170 days.
The Brotherhood of Steel repels the first wave of a mutant invasion, but a traitor in their midst causes the Citadel to fall. Fortunately, the advanced technology is mastered slowly by the mutants, and they were unable to use it against you.
With your assistance, Old Harold brings the ghoul population of the Hub into equality with the humans. The two sides work together, and the Hub prospers. Old Harold is still alive, as far as anyone knows.
Prerequisites: Take the Bloody Mess trait when creating your character (or picking up the Mutate! perk), procure bad Karma by the end of the game, or very quickly initiate combat upon exiting the conversation with Jacoren.
You march into the desert sands, leaving the shattered corpse of the Overseer behind you, never to return to the Vault.