Long before the birth of light, there was darkness—and the Dark Elves. Led by Malekith, they sought to use a weapon called the Aether to return the universe to that state during an event called the Convergence, when the Nine Realms align. Thor's grandfather Bor defeated them and hid the Aether where "no one would ever find it." Malekith and a handful of survivors escaped into suspended animation, waiting for the next Convergence.
Five thousand years later, Thor has spent two years restoring peace to the Nine Realms after the Bifrost's destruction scattered chaos across them. He's become a more thoughtful warrior, though his heart remains on Earth with Jane Foster. In Asgard, Loki is imprisoned for his crimes, visited only by his mother Frigga, who taught him magic.
On Earth, Jane investigates strange gravitational anomalies in London connected to the approaching Convergence. She accidentally stumbles through a portal to the Aether's hiding place. The Aether, revealed to be the Reality Stone in liquid form, bonds with her body. This awakens Malekith and his forces from their millennia of sleep.
Thor brings Jane to Asgard to separate her from the Aether, but Asgardian science cannot remove it without killing her. Malekith attacks Asgard directly, seeking the Aether. In the battle, Frigga is killed protecting Jane, devastating both Thor and Loki. Odin, consumed by grief and rage, wants to fortify Asgard and wait for Malekith to attack again, accepting massive casualties.
Thor devises a riskier plan: use Jane as bait, draw Malekith to the Dark World, and destroy the Aether once it's extracted. He'll need help escaping Asgard against Odin's orders. Reluctantly, he turns to Loki, offering him a chance at vengeance for their mother's death. "When do we start?" Loki asks.
The brothers share a rare moment of genuine connection as they travel to the Dark World with Jane. Their plan partially succeeds—Malekith extracts the Aether—but Thor cannot destroy it in time. Malekith absorbs the Aether and departs, leaving his lieutenant Kurse to kill Thor. Loki intervenes, stabbing Kurse from behind, but Kurse impales Loki in return. Thor holds his dying brother as Loki apparently perishes, telling Thor he didn't do it for Odin.
Thor and Jane discover a portal back to Earth, arriving in London just as the Convergence reaches its peak. Malekith begins using the Aether to spread darkness across all realms simultaneously. Thor battles him across multiple worlds as portals randomly shift them from location to location. Jane and her colleagues use their scientific equipment to disrupt the Convergence, ultimately teleporting Malekith back to the Dark World where his own ship crushes him.
Thor returns to Asgard and declines the throne, telling Odin he would rather be a good man than a great king. He's ready to return to Earth and Jane. But after Thor leaves, "Odin" transforms—revealing himself to be Loki in disguise. Loki faked his death and has somehow replaced Odin, now ruling Asgard from the throne.
In a mid-credits scene, Sif and Volstagg bring the Aether to the Collector, an eccentric being who hoards rare artifacts. They explain that the Tesseract is already on Asgard, and keeping two Infinity Stones so close together is dangerous. After they leave, the Collector muses: "One down, five to go."
In a post-credits scene, Thor returns to Earth and finally reunites with Jane for a long-awaited kiss, while a Jotunheim beast accidentally transported to London continues to rampage.