The Hyde Factor

The Hyde Factor is a Kim Possible fanfic by Erin Mills, in which strange things start happening to Kim after she accidentally gets injected with something during a mission to retrieve a stolen notebook. It turns out that the notebook originally belonged to Dr. Jekyll, and the injection is causing Kim to repeatedly transform into an evil alter ego (who takes the name "Faye Morgan").

Kim attempts to make the best of the situation, even trying to be as fair as she can to Faye without letting her hurt people. Unfortunately, it turns out that the transformations are unstable; either Kim's body will stabilize in one configuration (possibly turning her into Faye permanently) or the repeated stress to her system will kill her. Worse, Global Justice finds out about Faye, and the people who pull GJ's political strings have their own plans for her....

This story provides examples of:

 * Battle in The Center of The Mind: The final confrontation between Kim and Faye.
 * Berserk Button: When Ron tries to capture Faye in order to make one last-ditch effort to save Kim, she gets the better of him... until she tells him that she's going to kill his friends and family, concluding with Hana. Cue full-bore Mystical Monkey powered ass-kicking.
 * Broken Pedestal: The events of the story leave Kim with a lot less respect for Dr. Director and Global Justice.
 * Darker and Edgier: Obviously, with a Government Conspiracy using Global Justice as a tool for its Dirty Business so that they can gain control of a brutal sociopath, presumably for the purpose of using her as a weapon.
 * Dirty Business: After ICAD One orders her to capture Kim, Dr. Director reluctantly obeys, considering that a lesser evil than having ICAD One take over the operation directly.
 * The End or Is It:
 * That said, the author's notes at the end of the story say that no sequel is planned.
 * Et Tu Brute/What the Hell Hero: After the crisis is past, Kim firmly calls out Dr. Director for selling her out and allowing Global Justice to be corrupted.
 * Find the Cure
 * Godzilla Threshold:
 * Government Conspiracy: ICAD.
 * Hired to Hunt Yourself: On behalf of his son, Señor Senior Senior asks Kim to find the person responsible for putting Bonnie in the hospital... and turn the culprit over to him rather than the authorities.
 * How We Got Here: The first chapter is a scene from fairly late in the story -- Kim transforms during a fight with Shego, after which Ron finds Shego beaten nearly to death and a flippant note from Faye. The next chapter is set three months earlier, and describes the mission in which Kim gets injected with the transformation formula.
 * Jekyll and Hyde
 * Just Following Orders: Will Du's attitude when ICAD One removes Dr. Director and puts him in charge of Global Justice.
 * Kaleidoscope Eyes: Kim's green eyes change to violet when Faye is in control.
 * Loophole Abuse: Kim is able to get Faye to agree not to kill anyone, and to leave certain people completely alone. There are a lot of nasty things you can do to someone without killing them, and Bonnie isn't on the off-limits list....
 * Mugging the Monster: Bonnie makes the mistake of hassling Kim just as Faye is about to take control.
 * Power Dyes Your Hair: Faye's hair is a dark shade of red instead of Kim's red-orange hue.
 * Save the Villain: When Faye takes control during a mission, Ron does some fast talking to convince her not to kill Duff Killigan.
 * Split Personality Merge: When Kim's mind and body stabilize after her final internal struggle, she retains some of Faye's enhanced strength and senses. The final scenes indicate that, while she's basically back to her old self, her personality has become a bit more tough-minded and hedonistic
 * Split Personality Takeover
 * Stop or I Shoot Myself: Faye threatens to kill herself (which would of course also kill Kim) if Kim tries to cure the transformations.
 * Super Powered Evil Side: In addition to being more ruthless, Faye is significantly stronger than Kim. Faye also has extremely sharp senses.
 * Talking to Themself: Kim and Faye originally communicate via recorded messages; later, Faye is able to remain awake and hold an internal conversation when Kim is in control.
 * Theme Initials: Averted. When Kim's alter ego realizes that she needs her own name, she specifically rejects "that idiotic 'different name, same initials' crap".
 * A True Story in My Universe: When Ron asks Lord Utterson for more information about the notebook he'd asked Team Possible to recover, he explains that The Strange Case of Doctor Jekyll and Mr. Hyde was based on events in which his great-grandfather (the "Utterson" of the novel) was involved. The notebook was Dr. Jekyll's, and had been in the Utterson family's possession until DNAmy stole it.
 * Undead Tax Exemption: Justified. Wade creates a separate documented identity for Faye, as part of Kim's effort to keep Faye's existence secret and to persuade Faye to accept some limits on her behavior.
 * Villain Exit Stage Left: When Faye escapes and starts mowing down GJ agents, ICAD One bugs out.