The Initiate enters the town of Carbon based on information that the Brotherhood of Steel is on a mission in this area. Eventually, he or she will learn that the Brotherhood of Steel Paladins moved on to the town of Los in pursuit of the super mutant army lead by Attis, and technology hidden in a Secret Vault.
In Los the Initiate will find that the Brotherhood Paladins did not survive, and the only surviving member Rhombus is in need of help.
Richard claims to know the whereabouts of the Brotherhood of Steel Paladins and tasks the Initiate to clear the radscorpions from the Carbon warehouse before he will provide the information. As the Initiate is dependent on others to go anywhere in the game he must complete this task.
After a task to gain the Mayor's trust, Richard informs the Initiate that the Paladins went into the Carbon Crater and gives the Initiate an elevator key to go in after them. The Initiate must then search the crater for the Brotherhood, a quest that ends in futility. At the bottom of the crater the player finds that the information provided by Richard was false.
Running out of leads the Initiate eventually makes his way to the Carbon Mill and the raider Matron, Jane, where he witnesses a discussion between her and the super mutant Attis.
After witnessing the confrontation between Jane & Attis the Initiate will be spotted by Jane, she will then challenge the Initiate about destroying her soldiers. During the Initiate's questioning she will claim to be working for the Brotherhood of Steel, saying that she is offering information on Attis' army in exchange for protection and the Brotherhood turning a blind eye when it comes to her dealings with the townspeople and the mutants. She mentions that after her meeting with the Brotherhood that they went on their to pursue the Mutants in a ghoul city, later revealed to be Los.
Once the Initiate travels to Los he or she follows the lead from Jane that the Brotherhood are seeking out the super mutants to defeat them. He searches Los for the Brotherhood Paladins, but finds only Rhombus still alive.