The Enchantress slowly corrupts June, who besiesges Midway City and attempts to unleash her brother, the Incubus. The Suicide Squad is sent by Waller to investigate and aprehend the Enchantress as a potential asset. The Joker and his men find out about them and shoot down their helicopter in Midway City, leaving them stranded with only the Bravo 17 Navy Seal unit as mission support.
Boomerang encourages Slipknot to escape, and Waller detonates a bomb in Slipknot's neck, killing him. The team is then ambushed by monsters sent by the Enchantress and pursued to an abandoned building, but eventually escape with Diablo's help.
The team proceeds to the Enchantress' whereabouts in the subway line, while also being pursued by the Joker and his men. The Enchantress unleashes the Incubus, with Monster T as his host, and then kidnaps Waller to retrieve her heart and unleash Hell on Earth. With Waller compromised, the team is given an opportunity to escape, but decide to stick together and save the world.
The Joker kidnaps Harley and attempts to force her to return with him, but she refuses, and he escapes when the others come to rescue her. The Suicide Squad confronts the Enchantress in the Museum of Natural History, where Deadshot rescues Waller. Harley destroys the heart, freeing June from the Enchantress' influence, and Flagg saves June while El Diablo sacrifices himself to destroy the Incubus, saving the world and earning his redemption.
Waller has the surviving members of the Suicide Squad arrested once again, although Batman later arranges a meeting between Deadshot and his daughter in prison. She conscripts Deadshot, Harley, Boomerang, Croc and Katana to further missions under Flagg's command.
In the end, the Joker breaks into Belle Reve to rescue Harley, still smitten after she stood her ground and denied his every whim, and they lock eyes and smile.