The whole story starts with batman flying in his BAT ends up crashing as he is hit by where superman is hypnotised by a new villian called PIRATE.Then flash comes in rescue and saves batman from getting killed.Right now PIRATE is the best tactian alive as he comes from the parallel universe.He finds a cure for superman so he becomes unstoppable as cannot be stopped with kryptonite.
NOW batman is in pain both physically and mentally
He has to find a new way to get to superman to save him.
But he has no way to get through him with kryptonite then finds a solution.
Then he tells flash to do a tornado run as he can travel faster than light,so he goes back to past and see who the pirate was. He was none other than ra's al ghul he just wants to take revenge on the destruction of league of shadows by bruce wayne.So flash returns back with the antigen which was inserted into supermans body using kryptonite.