Master Khan is a member of the Foot Clan, first encountered by the Turtles when they got transported into the not so distant future by Viral, a dark future with 3 Shredders (Utrom Shredder, Tengu Shredder, and Cyber Shredder) at war with one another.
Khan apparently comes from the ranks of the Foot Elite, the personal bodyguard of the Utrom Shredder. After he was gone, and Karai, his adopted daughter, had given up the leadership of the clan, Khan jumped at the chance to become leader and led the illegal actions of the Foot, where he also lead a secret war against Hun and the Purple Dragons. One of his actions was the opening of a karate school where he put his pupils under hypnosis, so they would commit crimes for him. However, one of these students was Casey Jones, a close friend of the Turtles
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, ordering him to destroy the Turtles. From this encounter an intense personal antipathy between Casey and Khan also developed.
Shortly after Khan was contacted by the Cyber Shredder, who also worked on his escape from cyberspace, Khan took up as the right hand of this new incarnation of his old master. Khan began to support the Shredder in his plans, and finally succeeded in moving him into the real world. When the Shredder lead the Foot Clan against the Turtles and their friends who were celebrating the wedding of Casey and April, the Cyber Shredder was defeated by Donatello; Khan was also beaten and was captured by Casey.(Wedding Bells and Bytes
Khan also appears in the Mayhem From Mutant Island webisodes. Khan managed to return to the Foot Clan. 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.
In addition to his skills as a ninja fighter Khan has also increased speed and reflexes and can outmaneuver an enemy by seemingly disappearing before their eyes. This ability allows for the conclusion that Khan is a former member of the Foot Elite, who had a similar ability.
◾ 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 both a history/rivalry with Casey Jones (the first being the Purple Dragon leader, 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 this was never confirmed and he lacked the glowing red eyes and the teleporting trick the Elite had. Also he has the same voice actor as the main Foot Elite in the City At War episodes, though not exactly the same voice. ◾ Khan may have been named after 4Kids chairman Al Kahn. ◾ He is the second Shredder second in command to share a name with a famous conqueror (Genghis Khan). The first one being Hun (Attila the Hun).