Deadshot and Harley Quinn meet early when Deadshot is assassinating an inmate that is being transported from Arkham. Quinn disrupts the hit when she tries to break Joker out and both are captured and taken to Amanda Waller’s prison.
Waller has Joker moved to the prison as a means to keep Quinn in check. He spends most of the film in a cell, very much like Hannibal Lecter, until he breaks out in the end.
Boomerang is already in the Squad and there is a contention between he and Deadshot, Deadshot killed his father.
The team is tasked on a mission to prevent ‘bio weaponry’ from being sold to Lex Luthor by a human trafficking gang. The gang is handing over the Enchantress to Luthor who it is implied wants her for magical abilities. They kidnap her and take her back to the prison where she is kept in an underground area, which has all sorts of genetic freaks imprisoned including a King Shark.
Rick Flag is there as a watchdog over Waller. The twist is his character is revealed as being in league with the villain, Rick Flag Snr at the end. (This is what I believe may have been the reason Hardy left) It is out of left field. They want the weapons that Waller has amassed.
There is a lot of action in the script but it primarily deals with Deadshot, Harley Quinn and the Joker. Flag is more of a government agent than anything else before his reveal as a villain.
Check out the second source here: Latino-Review