In London, Dedede’s good-natured daughter Lori Loud grows estranged from her father especially after Apprentice Engineer Alpha (TOME) informs her that Dedede pushed Steven down the chute and they learn that the guy’s energy project in the re-purposed St Paul’s Cathedral is more than it seems. Connie and Steven travel on Dani’s airship, the Jenny Haniver, to the airborne city Airhaven, meeting other Anti-Traction League members. After questioning Connie, Steven realizes that Priyanka discovered a computer core for MEDUSA, a quantum energy-based superweapon used by the belligerents during the Sixty Minute War to instantly destroy entire cities, albeit shattering the Earth's crust into a thousand pieces that have rearranged the former continents. The Guild of Engineers has stolen the remaining components from Steven’s museum workshop and built a MEDUSA under Dedede’s orders. Big Mac catches up with them which results in a fierce skirmish that critically wounds him and destroys Airhaven.

Realizing that Connie is in love with Steven, Big Mac spares Steven and frees her of her promise before perishing. As Connie, Steven, and Dani travel to the Shield Wall of Batmunkh Gompa with the surviving Anti-Tractionists, Dedede kills Execk in a coup and musters support from Londoners by vowing to destroy the Shield Wall with MEDUSA and lead them to a new Hunting Ground in Asia. Dani convinces Shan Guo's Governor Samurai Jack to launch the Anti-Tractionist airship fleet against London but MEDUSA destroys the fleet and blasts a hole through the Shield Wall. After coming upon a stone carving of Medusa, Connie  discovers that her mother's necklace hides a "crash drive", a kill switch for MEDUSA. Connie, Steven, Dani, and the remaining Anti-Tractionists lead a raid against London, braving the city's anti-aircraft guns.

Connie and Dani infiltrate St Paul's and though Dedede mortally wounds Dani during a sword duel, Connie destroys MEDUSA with the crash drive. In a last-ditch attempt to destroy the Shield Wall, the insane Dedede has his henchmen kill the city's control crew and put the city on full throttle on a collision course with the Wall with no concern for all involved. With Lori’s help, Steven uses the Jenny Haniver to destroy London's engine. Connie catches and fights Dedede aboard his airship where he reveals that he is her father. Steven rescues Connie and shoots down Dedede’s ship which is crushed by London's slowing tracks, killing Dedede. With Dedede dead the surviving Londoners, now led by Lori, make peace with the Anti-Tractionists of Shan Guo. As Governor Samurai Jack welcomes the Londoners, Steven and Connie embrace each other and leave in the Jenny Haniver together to see the world.