In 1985, a medieval-themed party takes place in Wisconsin, USA. Hunter C-20 and her team arrive, having detected the presence of a time variant—Loki. However, the time variant Loki ambushes Hunter C-20 and takes control of her mind. Under Loki's influence, C-20 turns against her own team and eliminates them before losing consciousness. The variant Loki then takes the time-resetting device and a controller from one of the Minute Men, using a time portal to abduct Hunter C-20.
Meanwhile, at the Time Variance Authority (TVA), Loki is boredly undergoing training via Miss Minutes, a holographic projection. Agent Mobius arrives and gives Loki a TVA uniform. Mobius then takes Loki to investigate the recent attack. Hunter B-15 presents evidence, including temporal aura data, suggesting that the time variant responsible is another Loki. Mobius further reveals that the TVA has encountered multiple versions of Loki throughout history.
Mobius and Loki arrive at the crime scene to investigate. Loki claims to have found a clue but demands assurance that he won’t be eliminated once the time variant is captured. He also insists on being taken to see the Time-Keepers. Mobius realizes Loki is manipulating them and orders the timeline to be reset. Loki’s uncooperative behavior catches the attention of Judge Ravonna Renslayer, who calls Mobius into her office to discuss the case. Renslayer expresses doubt about Loki’s trustworthiness, but Mobius believes Loki might be capable of change. Renslayer reminds Mobius that Loki has always been deceitful on the Sacred Timeline and that only the Time-Keepers can truly judge him. She also reveals that the Time-Keepers are closely monitoring this case, something she has never seen before.
After Mobius leaves Renslayer’s office, Loki tries to justify his actions during the investigation. Mobius sees through Loki’s plan, accusing him of wanting to get close to the Time-Keepers to manipulate them and eventually take control of the TVA. With his intentions exposed, Loki questions why Mobius still wants his help. Mobius explains that he wants to solve the case quickly and that he pities the scared little boy he sees in Loki—a child shivering in the cold, deserving of compassion.
Mobius tasks Loki with reviewing all case files to find clues. Bored, Loki approaches the TVA librarian for information about the Time-Keepers and the Sacred Timeline but is denied access due to insufficient clearance. While reviewing his own file, Loki discovers a report about Ragnarok. He immediately shares his theory with Mobius, suggesting that the TVA has been unable to capture the time variant because the variant is hiding in apocalypses—events where their actions won’t create new branches in the timeline. To test this theory, Mobius and Loki travel to Pompeii in 79 AD. Loki’s experiment proves his theory correct.
Back at the TVA, Mobius explains to Loki that everything in the world will eventually be destroyed. Loki subtly tries to persuade Mobius to rebel against the TVA. Suddenly, Mobius remembers a clue—blue candy that only existed between 2047 and 2051. This narrows down the time variant’s location to that period. By cross-referencing natural disasters during that time, they pinpoint the variant’s hiding place to Haven Hills, Alabama, in 2050.
Mobius and Loki lead a team to the Roxxcart supermarket in Haven Hills. Upon arrival, they split up, with Loki paired with Hunter B-15. They notice a suspicious customer buying flowers. When B-15 approaches her, the variant Loki takes control of the customer’s body and then possesses B-15. Through B-15, the variant tells Loki, "You are me." Loki proposes an alliance to overthrow the Time-Keepers, claiming he has gained the TVA’s trust and needs a competent partner. The variant, who prefers to be called "Randy," shows no interest in Loki’s plan and instead possesses a supermarket employee. Loki questions Randy’s motives and discovers a time-resetting device hidden on a shelf. Suddenly, a possessed strongman attacks Loki.
Meanwhile, Mobius finds the kidnapped Hunter C-20, who is traumatized and disoriented. She reveals that she accidentally told the time variant how to find the Time-Keepers. Meanwhile, Randy—who is actually a female Loki—activates multiple time-resetting devices, causing the Sacred Timeline to branch into countless new realities. Chaos erupts at the TVA as the timeline fractures. The female Loki takes a time controller and escapes through a time portal. Mobius arrives just in time to witness Loki hesitantly follow her through the portal.