In Bishop's Gambit, Bishop tries to complete an army of clone's by capturing Master Splinter, and taking a DNA sample from him, leaving the turtles to escape death at the hands of his agents, and stopping his plans.
This episode is really cool for a multitude of reasons, the first of which is that Bishop reveals the full extent of his plans. I find it neat how he admits he has a secondary goal to wipe out half of mankind in order to keep Earth's population under control. It shows good development, and is also pivotal to the Bishop storyline.
It also gives birth to a new villain, The Rat King, which, in this, is a super human clone of Agent Bishop, although he technically isn't the Rat King until season 4. The action scenes and animation in the episode also prove fantastic. This episode, overall has little flaws, and is great.