Through the intro we know how the Ultimis Crew got to classifieds, but since there was no actual Easter Egg storyline for classifieds, I'm really confused about the start of the ending cutscene.
How did the the US government manage to trap the Ultimis Crew? How did the zombie outbreak in the Pentagon stop? Why did they put the Ultimis Crew together in a comically large cage without any guards?
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The storyline you’re asking about is hidden in various audio logs in this map. To sum it up:
The Ultimis crew you see in the ending is not the same one you play as. The ending crew is the one who survived the events of Moon, and they found a way to teleport to Earth, but they end up back in 1963, before Classified/Five takes place. The government detained them, while Richtofen’s body was taken in as it was lacking a soul (Samantha at this point was taken into Agartha by her father due to him gaining control of the Aether in Buried).
However, after that a zombified Richtofen (from post-Buried events, the same one you see in the Victis comics) arrives at Groom Lake, and interacts with the comatose Richtofen’s body, essentially transferring his soul from the zombified body to the regular one, and restoring him. He was then put in the cell with the rest of Ultimis. And that leads to the ending cutscene.