Ages ago, Malekith led the Dark Elves to destroy the Nine Worlds and return the universe to darkness. Armies led by Bor, Odin’s father, stopped the villain from gaining the Aether, which would have given him power. Malekith was vanquished, and the Aether was hidden away…
Thor is busy pacifying the Nine Worlds while Jane Foster pines for him in London. Anomalies lead her and Darcy to a deserted building in the city where a portal has opened up to another world. She is pulled through and lands in the hiding place of the Aether which possesses her; its reawakening also rouses Malekith and his minions from their long hibernation, and he immediately makes plans to destroy everything.
Heimdall alerts Thor that Jane has vanished from his sight so the hero arrives to rescue Jane and after an awkward reunion he takes her back to Asgard for safekeeping. Malekith springs his trap: He allows several of his men to be captured and in Asgard’s dungeon one of them turns into Kurse and breaks out to start a distraction while he dispatched ships to assault the palace from without. Malekith and Kurse come for Jane and Thor’s mother Frigga is killed protecting her. Thor manages to burn half of the villain’s face, but they escape.
After her funeral, Odin plans to build up Asgard’s defences to await the Dark Elves’ inevitable return. Thor suggests they go after Malekith to prevent disaster in Asgard but the old man won’t listen. Thor hatches a plan with the aid of Heimdall, Sif, Volstagg, and Farndral so that he, Jane, and Loki can leave the city and find another way into the Dark World to face their enemies.
Once in the Dark Elves’ realm, Loki betrays Thor, but it is all a ruse to deceive Malekith. There is a battle, and Loki kills Kurse but at the cost of his own life. Meanwhile, Malekith absorbs the Aether from Jane, Thor cannot destroy the powerful ancient element (it's an Infinity gem), and the villain departs.
Stranded there, Thor and Jane discover a portal back to London. There, Dr Eric Selvig discovers from the readings that the conjunction of the Nine Realms is imminent and it will centre on Greenwich, England. With the help of Darsey and her student assistant, the scientists install some device to stop the villains.
Malekith parks his flagship in the Earth (London), and battles Thor as the borders between the worlds become fluid. Thus military jets zoom into Vanaheim, and a monster from Jotunheim is loose in London.
After a long and hard fight, Thor impales Malekith with one of Selvig rods and stamps him to his ship with Mjolnir, just as Selvig transports the villain and ship back to the Elves world, where Malekith is seemingly killed when the ship collapses and crushes him.
Thor returns to Asgard where Odin offers him the throne; Thor politely declines, preferring to return to Midgard to protect the Nine Realms from there. Surprise: it wasn’t Odin but a disguised Loki.
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Mid-credit sequence:
Sif and Volstagg entrust the box containing the Aether to the Collector. After they leave, he reveals that it is one of the Infinity Gems and he only needs five more…
Post-credit sequence:
Thor returns to Earth to be reunited with Jane; meanwhile, the huge monster from Jotunheim is still loose in London.