In the Boss fight where you must defeat the Shredder, instead of focusing on the many Shredder clones, try fighting the real Shredder. He just stands still while his clones fight you. One attack that works well is Don's team move that shocks any enemy near its radius. Approach him close and use it. It will shock the clones and him, and he will not be able to attack. Change to Raphael because he fights the hardest and attack the Shredder a few times until he recovers. When he recovers repeat the steps until he is defeated. After this level the Foot clan, use a similar tactic when a Foot commander calls in more Foot ninjas as you defeat them. Use the same tactic on him. If you do not he will overwhelm you with hordes of Foot ninjas.