When the Turtles met him in the present, they found out that he was Casey Jones's karate teacher who hypnotized the students in his class to do his dirty work. April O'Neil was suspicious and asked the Turtles to check it out. The Turtles find out what he was doing and fight Khan and Casey, who was at the time hypnotized. They found it hard to defeat him because he knew the way they fought from Casey. Eventually, they escaped and Khan received a message from the Shredder, who's return Khan had been waiting for. Khan would continue to work as Shredder's right-hand man. (Back To The Sewer) TMNT in Mayhem From Mutant Island
Khan also appears in the Mayhem From Mutant Island webisodes. He is shown to still be running a fraction of the Foot and plans to take over control of New York by attacking the city.
There is somewhat of a running gag, where Khan gets hit/knocked/thrown by someone or something, causing him to hit something very hard (wall, Steel beam, light post, etc.), then fall to the ground (sometimes knocking him out cold) defeated. However, he usually recovers without injury (other than his wounded pride).
He is the second Shredder henchman to have a both history/rivalry with Casey Jones (the first being the Purple Dragon, Hun the Utrom Shredder's former 2nd-in-command).
It is hinted that he may have been one of the Elite Foot Ninja, for the same theme is used when Khan appears that when the Elite Foot appear. Though he lacked the glowing red eyes and the teleporting trick the Elite had. This was never confirmed. Also he has the same voice as the main Foot Elite in the City At War episodes.
Khan may have been named after 4Kids chairman Al Kahn.