My take, in more detail (events stick with what already happens in movie, except where noted);
-Start the movie off with a gang of punks robbing the mall, and Keno Spots them. He manages to knock a few out, but they get the drop on him and it looks like it's curtians. When something knocks one of the gun-toting punks away, and we get a serious ninja fight sequence (instead of the cartoony slapstick one from the film) As the groggy Keno comes to, he catches a glimpse of the mysterious green ninjas who saved him as they vanish.
-The turtles celebrate back at April's apartment, where April makes a remark that things between her and Casey 'didn't work out', dismissing him from the film. Meanwhile, at a dockside Warehouse that serves as the foot's fallback HQ, Tatsu (still sporting a bruise on his noggin from the fight with Casey) gathers the remaining foot ninja that didn't get picked up by the police or desert the clan, and swears revenge on the Turtles for killing thier 'father'.
-When he demands if anyone will step forward and challenge him, a shadowy figure emgerges in the warehouse, and kicks Tatsu's rear. But this is not Oroku Saki, who was actually crushed in the garbage truck here. No... this is Oroku NAGI! Saki's older brother from Japan who had discovered his brother's death, and now wants revenge. Tatsu is confused- he had head Nagi had been killed years ago- but as he seeks the Same goal as the dead Saki's brother, he accepts Nagi's leadership. Nagi dons the Armor and becomes the new shedder, and after hearing of the turtles and the reporter, sends a foot ninja to spy on the Reporter as april's cameraman.
-April does a report on TCRI labs, where Professor Jordan Perry is doing a toxic waste cleanup operation which he's not telling April the whole truth about. We then see Perry back at his lab, disposing of the last known canisters of mutagen from the batch, and talking to a bunch of his rats in the maze. We get the idea Perry prefers them, to his fellow humans who so carelessly buried the toxic waste years before. After the little song and dance where a suspicious Keno discovers the turtles, and the discovery of the new lair, Splinter sees the news report on TV and sends the turtles to investigate. Seeing a mutated flower from the site his spy brought him, Shredder sends Tatsu and the foot to the lab, where after a pitched battle with the turtles they take both Perry and the ooze.
-When shedder discovers 'the secret of the ooze', he has his foot ninja steal a rhino and a warthog from the local zoo, and shredder has them mutated into two fierce monsters- rocksteady and bebop, who have animal intelligence and are not idiots (Perry names them after his two favorite musical styles). Keno goes on a uncover mission to the foot, that ends up with the turtles coming to his rescue. While they handle the foot ninja easily, the two mutants beat them sensless, and force the turtles to flee- but not before they rescue Professor Perry and Keno. Shredder is impressed by how Rocksteady and Bebop sucseeded where the foot ninja failed.
-Perry tells them how the ooze was an accident, and they agree they have to get the ooze away from the foot. After having his two 'pets' that impritned on him rampage and kill dozens of people throughout the city, Shredder challenges the turtles to a final battle at the Docks. (I picture the two appearing like they did in that early Eastman and laird concept art from OT- dangerous monsters clad in scraps of armor, instead of street punks)
-Meanwhile, Tatsu confronts Nagi about rebuilding the foot after the Turtles and the Rat are killed, and Nagi reveals he has no intention of doing so. He tells Tatsu that the Foot had thier day, and a ninja clan must adapt and take on whatever new waepons and strengths will allow them to win. Nagi tells Tatsu that he and his human foot have served thier purpose, and he will rebuild the clan with an army of mutants! Futhermore, Nagi tells Tatsu that he was the one who convinced his younger brother that he had been dishonored by Yoshi and Tang Shen, and commanded him to follow his former friend and former love to new york and take thier lives. Nagi stared the whole cycle of vengence to make a man out of his brother, by having Saki eliminate Shen- his only connection with love or any other sort of human emotion. Feeling betrayed, Tatsu attacks Nagi, who quickly kills him. Drinking a small vial of the ooze, Nagi begins to transform...
-The turtles, April, Keno, and Perry comes to retieve the ooze, only to find the foot being all killed by Rocksteady, Bebop, and the newly mutated Super shredder. The Turtles duke it out with the three mutants in an epic battle, while Keno and April plant Donatello's explosives all over the piers the way donnie instructed them. The canister of remaining mutagen is knocked from Super Shredder's grasp, and shatters on Perry as he tries to retieve it. The professor flees with his face burning from the ooze. Finally Donnie sets the explosives off just as the turtles jump clear as all the docks explode, and the three mustants are sent flying and swept out to sea. With the New york Foot entirely wiped out and both of the brothers Oroku dead, it seems the Turtles Splinter, Keno, April, and the turtles return to the new lair to celebrate, with Splinter declaring the cycle of revenge has finally come to a close.
-In another part of the sewer, we see a scarred and mutated Professor perry, all covered in rags and bandages and swearing that his revenge has just begun. And all around him, are swarming the rats of the sewers, awnering the call sent out by the mutagen-given powers of thier new king...
...and that's what I would've done! The whole mirage cycle of vengance, with OT elements thrown in for the kiddies!
