With Clayface's mutation, he had a plan, with being able to perfectly duplicate people, Clayface was essentially blackmailing the rich, until he came across Wade, who refused to cooperate, thus Clayface framed him for murder. This of course brought Batman into the picture, so in order to keep his scam going, Clayface decided to target Bruce Wayne, in an effort to get to Batman, so he could touch him, then reveal to the world who Batman was, ending him once and for all. Not the worst plan.
Unable to escape Clayface, Bruce ends up getting swallowed up by the monstrous man, and dropped into a trash compactor with Lucius fox, Star Wars style. Inside, Bruce and Lucius are surrounded by scrapped prototypes, with no way to get out, until Bruce finds one particular prototype suit, one that's pitch black with a red bat emblem, and uses it to bust a hole in the wall. When Bruce asks why Lucius scrapped it, it's because the suit wouldn't be cost effective until twenty years from now... hint, hint. Despite Lucius suggesting Bruce seek medical attention, Bruce tells his old friend he's fine, and to contact Batman, while he "talks with the police.
Elsewhere, Clayface is disguised as Bruce, on the run from the cops, whose motorcycles he trips up with the use of his powers. He arrives at a Wayne Enterprises building, but his elevator stops on the wrong floor, where he's greeted by a punch to the face from Batman, who is wearing a full body suit, with no flesh exposed. The two begin to fight, but none of Bruce's old tricks to deal with Clayface work, and eventually leads to him getting his ass kicked, and his mask cracking. The cops arrive just as Clayface manages to touch Batman's chin and reveal that Bruce Wayne is Batman.
Once Clayface lets go, Bruce signals Lucius to drop a mini panic room over him, with no way in or out for Clayface, in fact, the only dna that would be able to trigger it opening from the inside would be Basil Karlo's, but due to Clayface's mutation, that's the one DNA he can never get back. It's no matter to Clayface though, as he addresses Bruce directly, apparently knowing his secret. But, Bruce trolls Clayface a bit, and pulls off a thin fiber mask from his chin, which he claims to have put Bruce Wayne's dna over, keeping his secret safe.
Clayface gets a bit agitated, telling Batman to go take care of his boyfriend, saying that Bruce Wayne is just another rich jerk who cares about no one but himself, as he starts to turn into Damian. Clayface mentions having come across Wayne and his son a few weeks ago, and could tell then that Wayne didn't even care about the kid, from the look in Damian's eyes. Bruce snaps, he goes rage mode, and just tries to kick in the chamber to get to Clayface before Gordon can calm him down.
Later, Alfred patches Bruce back up, and they discuss Clayface a bit. Bruce then moves on to Damian, telling Alfred that he's not going to lose himself again, but at the same time, he's not ready to let go yet. Alfred understands, and asks Bruce if he can watch too. Both of them put visors on, and watch the footage of Bruce and Damian's last mission together. As Bruce sheds a tear, Alfred puts his hand on his shoulder.
Then in the backup, Superman is having a rough time with the Will of the Whisp, while Bruce tries to comfort the girl whose soul is still trapped in the room. Bruce tries to get the girl to remember where the spell they used to summon the spirt was written down, pointing out how important it is to him, because Superman is one of his best friends, and they need to help him, so he can help her move on. The girl eventually gets it together, and helps Bruce find the paper they had the spell written on, which allows Bruce to cause the spirt to disperse.
With the spirt gone, the girl begins to fade as well, as she's now allowed to move on. Before she goes, she tells Superman to take care of Batman, because he's a lot sweeter than he looks. When they're alone, Bruce tells Clark he's not ready to talk about Damian, but thanks him for showing up anyways. Bruce then offers Clark the opportunity to stay on patrol with him, but pulls his famous disappearing act.