The first mission was to rescue Waller but it wasn't made obvious to the team, basically because it would be highly doubtful they would have gone for it, seeing as it was Waller that pushed them together with threats. She planned to use them to basically cover up the fact she'd screwed up first with the Enchantress (which was why she shot the remaining people in the command centre with her, a rather 'evil' and self serving thing to do).
At that point nobody else on the Squad ( apart from Flagg) knows that the Enchantress is respouncible for all the chaos , at least until Deadshot finds the 'Top Secret' file in Wallers bag after the helicopter crash ( I love it when they have 'TOP SECRET HIGHLY CLASSIFIED' emblazed upon the folder when a simple plain cover would be slightly more appropriate, but it certainly makes it easier to find though)
Waller ( your classic boss high achieving psychopath) would then use the team to cover up her murdering all her assistants and her complete and cataclysmic failure with the Enchantress. She just would not take the blame for any of it and was willing to burn everyone else to the ground to save herself and her career.
Thats ultimtely why the team then decide to tackle the Enchantress based on the fact Waller was in many ,many ways worse than them for what she had done and for once they could look like 'heroes' and not the bad guys. But shes in government soo.....not a bad guy then. I liked the way this morality was played with but it seemed to confuse a fair few of people.
Personally I was VERY disappointed that they did not use the Joker as the behind the scenes manipulator of the Enchantress chaos in order to get Harley free, ie setting up Waller to take the fall, trapping her, obtaining the heart off her so that at the very end that he was the ultimate 'hero'. Then escaping with Harley would have made more sense, rather than the ending we finally got. That was always the beauty of Nolans Joker, his apparent madness was anything but, he was a brilliantly manipulative master planner of chaos, by forcing people to make choices . Thats what I was expecting anyway and was a little annoyed that instead we had this rather crude madman.
PS
Apparently the 'Original Score' to the movie will be released later after the sound track album
PPS
Also ALOT of the Joker/Harley scenes were cut because of some EXTREMELY negative responses. You can guess why and from where. I know, I know, that's how its is in their comics history but these are modern times and whilst its alright to be an empowered, deranged and sexily dressed killer, its not OK that they are the victim of domestic abuse.
PPPS Interesting article here on Hollywood here
https://www.theguardian.com/film/20...sters-directors-star-wars-dc#comment-80595652