The Citadel at the End of Time is a place located at the end of time and the home of He Who Remains, the true creator and ruler of the Time Variance Authority. From this citadel, he observed all the existence and controlled the TVA without anyone knowing.
The Citadel at the End of Time is an old construction located on the top of an asteroid beyond the Void at the end of time. The entire building, with all its architecture, was carved in situ from the black stone with gold vein embellishments of this same asteroid.
Around the asteroid, the Sacred Timeline can be seen pulsating as a tangible force. The Citadel is abandoned and in ruins except for a light illuminating a window at the peak of the towering construction, the home of the creator of the TVA, He Who Remains, who settled there after the Multiversal War.
Because the timeline of the end of time is still not written, it is impossible to perform actions that would create branches which would be detected by Time Variance Authority. It is also not possible to get to the Citadel using a TemPad, because there is nothing that it will lock on to, so the only known way to get there is going through the Void. This makes this location a great hiding place for a Variant and the reason He Who Remains chose to stay there. He Who Remains also has Alioth, a creature that he settled in the Void to devour the branched realities that the TVA prunes, guarding the only way into the Citadel. This makes even harder for anyone to find the Citadel, as they have to face a giant storm that can consume space and time itself.
Similar to the Void, because the Citadel is the end of time, inhabitants of this location never age, which is why He Who Remains doesn't look like an elder, despite the eons that have passed since the end of the Multiversal War.
In the fifth episode, the Citadel at the End of Time first appears when Sylvie is being chased by Alioth and briefly links with it, allowing her to see a glimpse of the Citadel beyond the Void and making her deduce that the creator of the TVA is using Alioth as a gatekeeper. Later, when Sylvie and Loki manage to enchant Alioth together, the clouds of the storm dissipate and reveal the Citadel in the distance.
In the final episode of the season, Sylvie and Loki trek cross the asteroid to get to the Citadel. At the door, Sylvie becomes nervous because she waited her whole life to have her revenge against the responsible for the Time Variance Authority which caused the destruction of her timeline. When the doors open inviting them in, the duo enters a dark atrium and as approach its center, the mascot of the TVA, Miss Minutes, suddenly materializes in front of them. Miss Minutes offers the duo a deal from He Who Remains, in which they can be back on the Sacred Timeline and have anything they want, including be together on the timeline, if they accept. The pair considers the deal, but ultimately refuses it and continue to explore the Citadel after Miss Minutes disappeared.
Walking inside the Citadel with their weapons drawn, the duo arrives at the Hall of Heroes. There, they find broken statues, Loki notices that they are covered in dust and wonders if the owner of the castle is still alive. However, the duo is surprised by the sound of the elevator suddenly operating and when its door opens, He Who Remains emerges from it. He invites Loki and Sylvie to come inside the elevator to go talk to him at his office. At the office, He Who Remains reveals that he has been observing them and knows everything, even their schemes and intimate moments they shared during their way to the Citadel. He also tells them that he was the one who paved the way for them to arrive there.
He Who Remains tells Sylvie and Loki about the Multiversal War caused by his own Variants, which made him reorganize the timelines into the Sacred Timeline and create the Time Variance Authority to stop them. He gives them the option to kill him and unleash his Variants in the multiverse, but also reveals that he has done his job for too long and has been looking for a successor, giving the pair the chance to replace him and rule the TVA. While they talk, the Sacred Timeline seen outside He Who Remains' office windows starts to branch and he confesses that they crossed the threshold, the point in time in which he does not know what will happen next.
While Sylvie doesn't believe in He Who Remains and still wants to kill him, Loki considers his story and tries to stop Sylvie from making a mistake. The duo fights inside the office, with Loki trying to prevent Sylvie to get to He Who Remains who is watching everything from his desk. After him blocking her blade with his body, Sylvie becomes emotional hearing Loki's words of care for her and kisses him, but still uses the TemPad on the He Who Remains' desk to send him back to the TVA. Sylvie then kills He Who Remains, and falls beside his corpse unsatisfied with her own action, while the Sacred Timeline outside is shown to be splitting into even more branches irreversibly.
At the TVA, Loki finds Agent Mobius and Hunter B-15 and tries to tell them that he and Sylvie had freed the Sacred Timeline after finding He Who Remains beyond the storm at the Citadel at the End of Time, but they don't recognize Loki because they are Variants from a new TVA ruled by Kang.
- The black stone from the asteroid which was used to construct the Citadel can also be seen in the Time Variance Authority headquarters. The statues in Ravonna Renslayer's office, the front of the judge's dais in the Time Court, and the elevator to the Time Keepers' chamber, were all carved from the stone of this asteroid, linking the place with He Who Remains who built the TVA.