Task-Force X is created in the 1940's, to use war criminals in suicide missions in exchange for reduced sentences. The team is led by Rick Flagg, who dies along with his men in a mission gone wrong, and the project is buried.
In present day, A.R.G.U.S. operative Amanda Waller decides to revive the program, using superhuman criminals that are emerging across the world to handle extraordinary threats. The military agree to support her, and she selects Flagg's son, Rick Flagg Jr., to lead the team.
The recruits are Deadshot, Boomerang, Killer Croc, El Diablo and Slipknot, who are all transferred from other prisons to Belle Reve. Harley Quinn is the last of Waller's list to be captured, after the Joker ditches her during a chase with Batman (which opens the movie, by the way).
They all accept the job, get their tracking bombs implanted on their necks, and meet their support team, the Bravo 17 Navy Seal team led by Scott Eastwood's character, Tom Tresser. Their first mission is to retrieve some stolen Kryptonian technology from the Battle of Metropolis from weapons dealers. Katana joins the team as Flagg's bodyguard.
Meanwhile, Waller employs Flagg's girlfriend, June Moon, an archaeologist, to investigate strange occurances that Waller believes might be connected to extraterrestrial activity on Earth. It leads her to ancient tombs, where she awakens and is possessed by the Enchantress, experience a string of SPOOPY STUFF before becoming a full-blown witch.
While June is going evil, the Squad "graduates" to official sanctions after their succesful test run and goes on a bunch of mission, leading up to retrieving chemical weapons acquired by the Joker. There's a big shootout at the Joker's nightclub (he's much more of a mobster in this) which leads to Joker finding out Harley Quinn is with the Squad. He then decides to get her back.