Shredder ordered him to create to mutant monsters with the ooze but Perry refused and later changed his mind when Tatsu threatened him. Perry created Tokka and Rahzar, but contaminated the ooze used to make them. Thus resulting in them being intellectually inferior and not dangerous beasts but they were still tough monsters even though they were newborns. Shredder wanted them destroyed after finding out they were inferior and childish but, in order to save their lives, Perry said they would be useful against Shredder's enemies (i.e., the Turtles) due to their incredible strength and child-like loyalty. Therefore, Shredder decided to keep them around.
The monsters thought Shredder was their mother since they couldn't say master right away. Perry was tied up again at some point and hidden in a junk yard house until Donatello saved him during their battle with the Foot and Shredder. Tokka and Rahzar fought the Turtles again in the construction site and in a night club near the river front. Perry helped the Turtles defeat the mutants and was around to get the canister from Shredder in the night club. Perry told the Turtles their origin but Donatello didn't believe their creation was a mistake. Perry also helped Donatello create a formula that unmutated Tokka and Rahzar in the night club battle.
Perry is in no other version of Ninja Turtles and even thought he's a brilliant scientist he is not another version of Baxter Stockman. Donatello becomes good friends with Perry in the movie and Perry is very fascinated with the Turtles and Master Splinter as well. Its an unknown factor as to what became of Perry after the movie ended but he might have returned to the T.G.R.I to continue his work. He's not in the first, third, or fourth movies at all.
Leonardo, Michaelangelo and Raphael do not understand Perry's and Donatello's idea on how to defeat the mutants. Shredder and Tatsu don't seem to understand Perry's genius either. Tatsu was a little bit scared of Toka and Rahzar when the first came out of their cells and walked over to Shredder. The Foot relied of Tokka and Rahzar to fight most of their battles in the movie while they watched it as if it was wrestling match.
Also important to note, the character was originally conceived as an Utrom. This was to be revealed as a cliffhanger or twist ending, but was nixed due to worries that the audience would mistakenly identify the Utrom as Krang.