The movie start with June in the cave, it's the origin story of Enchantress, then Smith's character try to rob something and get caught, then we see Harley's origin and how Batman caught her and put her in prison, then we see Waller come to her and tell her to join Tesk Force X and that's how we get to meet the rest of the Squad.
Then story is Enchantress wants her full powers back and to do that she needs two things - to bring her brother back to life, she finds a body and transfer his soul to it and they make people into monsters. Second thing she wants is her heart back and Waller has it, she tries to take it back from her. Squad tries to kill her and her brother, they fight the brother on a train like we see in the trailers. Diablo sacrifice his life and make an explosion that kills him and the brother.
Then the Squad gets to Enchantress who has Waller and her heart. They save Waller, Harley destroy the heart and Enchantress is defeated and "thankful" Waller put them back in their cells. End of the movie is Joker - who's mostly just in the background most of the movie and try to get Harley - breaks into the prison and gets her out, she sees him and smiles. End.