Hush told Batman that Alfred would die - the blood he'd been infected with would kill him. Only the blood of Cassius Clay could save the victims.
Just as Hush had hoped, Batman broke into Arkham to snatch the "pure" Clayface. He explained to Cassius what was going on and asked for his help. Batman was able to spray him with something so he would revert to human form. Police and SWAT attacked as Batman and Cassius exited Arkham. In the melee, Hush got three samples, but was smashed by Clayface. The new Clayface, working with Hush, confronted Cassius. After the battle, the new Clayface ended up with the sample. He gave it to Batman and asked that he save his family from Hush.
The detectives were given a warrant to arrest Alfred.
Bruce showed the detectives that the dead man (the new Clayface died) had near identical prints to Alfred. The case was dropped.

A detective visited Wayne Manor. The man who took care of Bruce's summer house had committed suicide. Wayne admitted he'd not been there in ten years.
He went down to check on everything and ran into the man's son (his wife had died months before). He also ran into tons of memories. He found letters written to his father from another woman. He set out to find her. That night, he watched all their home videos to see if he could tell his father was "faking it" with his mother. He tracked down the woman, who still worked at the hospital. At a charity event, he cornered her and they talked. She asked if he'd found the letters. Thomas had given them to Martha - they'd never had an affair.

Editor's note: this story takes place before War Crimes.
A traffic helicopter crashed into a bridge in Gotham City. A woman choked and died at a board meeting. A train engineer died, causing a derailment. All three turned out to have the same pacemaker - made by WayneTech.
Batman discovered their frequencies had been altered slightly to induce the heart attacks. Batman fingered Hush for the crime due to his medical background and his hatred for both of his identities. Hush denied doing it, and Batman believed him.
Joker played with two birds he'd gained companionship from when he was recuperating with the circus freaks. He'd been training them for some time.
Joker appeared in bed with a hooker, who'd picked up a surgeon as a john.

Editor's note: this story takes place before War Crimes.
After one more time being humiliated, Hush went after the Joker. He found him in Cobblepot's Iceberg Lounge. Joker flashed something at him and he went down. He'd been unconscious for three weeks - Joker had one of the controllable pacemakers installed in him.
Batman went after Joker, but had to attend a guard he'd shot.
Hush went to Bruce Wayne. Bruce agreed to help if Hush admitted himself to Arkham. He did. After the successful surgery, Elliot escaped. Batman caught up with him on a rooftop. Hush lectured him about killing and how many had died due to him not killing his "freaks." Batman still refused to let him kill the Joker. Batman insinuated there'd been no surgery at Arkham just before the Joker appeared.