After you deal with Wonder Tower head go tot eh marker on your map. Fight the snipers if they are making it tough to reach your destination. Keep proceeding onward & take down the other thugs as quietly as possible. Once they are dealt with head inside to fight Clayface.
Listen to what Batman says at the beginning of the fight, since it will help you in defeating Clayface. You need to toss freezing grenades while he attacks. Dodge his offensive movements & toss those grenades whenever possible. The fight is a long one, so be ready to dodge a ton. Keep your distance until he has become totally frozen. Then you go in & start punching him.
He will regain his movement & this time he will be a bit angrier. Just stick to what you did before to get to the third phase of the fight. You will now need to being fighting the smaller clay goons that spawn. Once they are dealt with, Clayface will reappear & you will need to toss the grenades into his mouth. After two or three grenades Clayface will be defeated.
You will need to go back to Catwoman’s apartment. Get through the fight & then go into the museum. Fight the thugs there & locate the gladiator room. Eliminate the thugs in this room to gain access to the door at the top of the staircase. Make your way into the caged section to reach the armory & a new predator situation.
You will need to keep your focus on Two-Face as his henchmen will keep appearing. Successfully take down Two-Face & you will be back in control of Batman. You can protect Gotham & complete the rest of the side quests as you see fit.