Hush fired Prometheus; Deathstroke's Kobra men captured him. Talia sent them after Hush. He was also captured. Hush was unable to cure him - he'd been infected by one of the Ivy clones. Talia promised him that if Prometheus died, he would, too. Hush got him stabilized and was able to escape.
The key they were looking for (which Talia believed Prometheus knew where to find) was uncovered in the JSA's headquarters.

A film student named Riley accidentally caught some shots of Bruce Wayne fighting Hush atop a nearby building. He compared it to some amateur footage of Batman and realized they were the same. He set his friend up to kill a security guard so they could get another tape. The friend was shot, too.
Riley gave a tape to Wayne. The boy wanted "millions." He refused to take favors (jobs, etc.) and demanded cash. Both he and Alfred (who was the middle man) were shot.

Weeks previous (while hiring a gang to kidnap Alfred), Hush found a chemical that could help the victim change shape like the Clayfaces. The chemical had caused a fire in a warehouse. "Tommy Elliot" went in search of a firefighter who'd survived the inferno.
Alfred remembered what he'd seen on the boat before being knocked overboard.
Riley, the man who'd attempted to blackmail Bruce Wayne, was found dead.

Six months previous, Hush stopped a man from jumping off a bridge to his death. The man had mutated while escaping a fire. Hush promised him he could cure it if he would help him destroy Bruce Wayne. He had the newest Clayface become him - Tommy Elliot.
Detectives were called in - two actresses notified them their director had been murdered. They found a bag of cash with Bruce Wayne's name on it.
Alfred told Bruce Tommy Elliot was a captive of Hush and not Hush himself. He insisted on going out with him on patrol. They got DNA from the boat - Batman learned it was not a "who," but a "what" - a new Clayface. Batman got a feed on Hush and went after him. They fought off the edge of a building; Alfred cut Batman's jumpline.

Batman was able to grab Alfred and help him regain his senses. Back at the cave, Batman did blood work on him and learned Hush had infected him with Clayface blood. Two detectives knocked on the door of Wayne Manor and told Bruce some of his belongings had been found in a dead guy's apartment. Since he had an alibi, they asked to speak to his "servant." Bruce told them Alfred was away. Bruce locked him up in the cave knowing he was the last person to see the director alive. Bruce spoke with Akins and found Alfred outside police headquarters. He took him home and went after Hush.
Hush realized he needed a strain of Clayface DNA that was not altered by human DNA. The only pure sample could come from Cassius.
Batman caught up with Hush and was taken by surprise when he ended up grabbing Clayface. The real Hush held a gun to his cowl.