The story revolves heavily around the Brotherhood of Steel and its pursuit of the Enclave. After its victory at the end of the original Fallout 3 story, the Brotherhood feels that it needs to strike while the iron is hot and wipe out whatever remnants of the Enclave remain. What it discovers is that the strength of the Enclave hasn't been diminished [as much as it seemed to have been], so players become an integral part of the skirmish.​

This was perhaps one of the toughest things for us to do when creating Broken Steel. We took great pains to make certain that the actions players made at the end of Fallout 3's original story are not completely invalidated. In fact, we took what players did into careful account and wove it into some of the quests. For example, if players decided to follow President Eden's advice and spiked the water with the Modified F.E.V., that decision will affect the Capital Wasteland and how the player interacts or perceives its inhabitants. We've also added some new decisions to the original storyline that players will be able to make to add some more variety and make the transition feel right.​

We didn't want to simply crank up the statistics of the same old enemies and call it a day; we wanted to create brand-new versions of them to give players a real sense of progression. A great example is the aforementioned super mutant overlord. He's a huge brute, but we wanted to give him a powerful ranged attack as well. None of the existing weapons seemed to fit the bill, so we've created the tri-beam laser rifle, which is an extremely powerful ranged laser shotgun.​

"Broken steel doesn't have an ending," he said. "There are no more endings, we got the message."

The game also slightly tweaks the moments leading up to the ending, adding the ability to send one of several of your companions to complete the final task of the game, instead of doing it yourself.
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In Broken Steel the battle between the Brotherhood of Steel and the Enclave still rages and you are tasked with discovering and helping to build a Tesla Canon, a new, more powerful weapon for the Brotherhood.
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The new area is packed with new enemies, including a super mutant overlord, a feral ghoul reaver and an Enclave hellfire trooper; new weapons, like the Tesla Canon and a projectile flame thrower; new achievements and even new perks. Hines only detailed one of the perks though, called Puppies! If you pick the Puppies! Perk when Dogmeat dies he gets reincarnated automatically as a puppy, which you can go to certain areas to add back to your group.​