Callie Maggotbone has created a clone of Mark Lilly to replace him in the Department of Integration's bowling tournament, as the real Mark is a "terrible bowler". The clone, who has blonde hair instead of brown, has a sadistic worldview and hides the real Mark in his closet. The following day, Twayne Boneraper has hired a new assistant Tad to do his dirty work. Tad's first action is to re-assign Callie, whom he thinks is a saboteur, to a useless department in sub-basement 37. Tad also cuts Mark's department's budget by 80%, but is rather impressed by Clone Mark's attitude. The next day at his group therapy session with Mark's students, Clone Mark turns it into a fight club to train them for the bowling tournament. Later, Clone Mark finds Callie's diary at her apartment and finds out that she plans to murder him after the tournament and then get the real Mark back. Infuriated, he decides to murder Tad and frames Callie for the crime by using a trident from her apartment as the weapon and leaving it at the scene. Callie gets hauled in by Francis Grimes and his crew, but Grimes finds Mark's behavior strange and decides to investigate further.
Grimes visits Callie at the prison, but she cannot reveal the truth because Clone Mark will kill the real Mark if she tells anyone that he framed her. Grimes goes to Mark's apartment and discovers the real Mark tied up in his own closet. However, Clone Mark appears behind him and shoots him in both his legs. Grimes, as he tries to fire back, ends up blinding himself. Clone Mark has grown tired of bowling and decides to leave the city. The next day, the real Mark is back at the D.O.I. and his students are in no condition to bowl since Clone Mark forced them to fight each other. Mark tries to free Callie from prison, but he must find evidence to prove her innocence. Mark finds his clone at a tropical island and he confesses that he killed Tad. The clone is then gassed to death and his body is scrapped for body parts, which gives Grimes new legs and eyes. At the bowling tournament, Mark wonders where his clone came from, and Callie says that he "will never know".
- The title card presents the episode as "Episode XX: Attack of Mark's Clone", parodying Star Wars Episode II: Attack of the Clones.
- Ending credits depict scenes from The Big Lebowski