Surreptitious Machinations
Surreptitious Machinations is the major plot line that takes up the entire fourth year of the web comic General Protection Fault, from November 2001 through October 2002. It is divided into nine chapters, plus a prologue and an epilogue both starring The Gamester, an extradimensional being that guards the many universes of all space and time, and his apprentice, Mischief.
The alternate timeline described in Surreptitious Machinations went as follows: Trudy Trueheart scattered the GPF employees and took over the world, using the trusting nature of Nick Wellington to build "Project Velociraptor" so it could power alien weapons she had acquired. The GPF crew reassembled and formed the resistance against the domination of Empress Trudy. They convinced Nick that he's being used and brought him back to their side, using his knowledge against Trudy. In the process, Nick and his then-former girlfriend, Ki Oshiro, reunited and fell in love again, resulting in Ki getting pregnant. Soon after their reunion, Nick was recaptured by Trudy's forces. When Nick refused to rejoin her, Trudy killed him, then went on a rage against the resistance, decimating them. Twenty years into the future, all that were left were Professor Wisebottom, Sydney Duncan, Socrates the slime mold, and Todd, who was Nick and Ki's son. Professor Wisebottom sent Todd to the present day in his time machine to PReVENT Trudy's domination, while Empress Trudy followed suit using a time travel remote to "educate" modern-day Trudy and initiate the domination.
Empress Trudy also sent a robot that looked like Jason "Fooker" Barker to the present to go on a [...] spree. The robot, dubbed "The Fookinator," was stopped by Todd, who arrived to the present just before, along with present-day Nick and Ki, who were unaware of Todd's identity. Still, the incident got the real Fooker sent to prison for Life. Trudy torched GPF software and framed owner Dwayne Duncan, getting him sent away as well. Ki and Nick ended up going their separate ways when Ki's father was mysteriously run down by a car and critically injured. Nick ended up working with Trudy at JCN Software, where she began using his Inventor's Gene to build Velociraptor for the Commune of Really Unscrupulous and Diabolical Evildoers (C.R.U.D.E.)
Ki was visited by future Todd, who revealed his future to her (along with the fact that she was his mother) and got her to reassemble the crew. This included Fooker, Dwayne and Trent Terrell (who all escaped a prison transport in a story similar to The Fugitive), Sharon Murphy (Fooker's ex-girlfriend), Dexter Smith (a former GPF contractor, and Sharon's recent ex-boyfriend), and the slime molds, Fred and Persephone. They worked together with the Undisclosed Government Agency (U.G.A.) on the day Trudy was supposed to take control.
Trudy and C.R.U.D.E. gave the United Nations an ultimatum: hand over control of all national governments within one hour, or they would use an orbiting satellite laser to destroy New York City. U.G.A. and the GPF crew foiled their plot when Sharon, using Trent's wireless PDA, aimed the satellite to fire harmlessly in the Atlantic Ocean. Fooker's next-door neighbor, Chuck, died when Trudy turned the mind-control device she was using on him up to full blast and threw the controller away. Dexter defeated a giant man twice as big as him, Mister Inertia, in hand-to-hand combat.
Ki got the proof of Trudy's plans and brought them to Nick to prove to him what's going on. He promptly renounced Trudy. She tried to kill him, pointing a gun at his head, but she could not pull the trigger. Trudy escaped as the news media (in particular, a television news crew based loosely on characters from the web comic Newshounds), receiving her journals and plans, started to expose the plot, including the evidence that would exonerate Fooker and Dwayne.
Dwayne determined at the end to rebuild GPF software, but Fooker, who was his system administrator, was transferred overseas by U.G.A. because his trial blew his cover. Dwayne hired Sharon to take his place. Fooker's transfer also meant that his relationship with Sharon, rekindled during the events of the previous year, would be put on hold until he could get back home.
Nick and Ki did reunite, but unlike the hurried romance of the alternate timeline, they appeared to have started their relationship where they left off.
Present-day Trudy was double-crossed by C.R.U.D.E., and went on the run.
In the end, their future undone, Empress Trudy and Todd began to FADE out of existence. Before she disappeared, Empress Trudy used her remote to time travel out. Todd appeared to phase out of existence himself, but he was saved by the Gamester and currently acts an an agent to handle affairs The Gamester can not. These are chronicled as a sidestory in the book version of Surreptious Machinations. Nick was never made aware that Todd was his son from the future, and still doesn't know.