Chaos from the Tamers Forever Series. Let's break it down, shall we? He has spent centuries manipulating humanity's most powerful figureheads in order to create worldwide chaos,. He is a ruthless tactician and a nigh unstoppable Badass. Not to mention being quite a hit with the ladies. (Although how much of that last part is simply his own bragging is up for debate). And he tops it all of by being witty, funny, charismatic and all in all, just a joy to watch.
A few chapters later, Fuyutsuki invokes the trope by name when Gendo returns to power.
Loki, the Big Bad of My Little Avengers, who has the rather telling nickname of "The Magnificent". True, he probably gave himself the title as a bit of ego stroking, but he definitely lives up to it. At the climax of the story, he reveals that the entire plot up to that point was a Gambit Roulette: by removing Celestia as a potential threat via depowering her, he causes a Mass Empowering Event that lays the potential for the world ruled by magic he's long envisioned, and more importantly insures that Big Mac will end up with teammates — teammates that Loki can threaten in order to force Mac to surrender Thor's powers to him. And it works perfectly, with him only being defeated afterwards due to Pinkie being a bigger Spanner in the Works than anticipated. He also shows that he anticipated Trixie's betrayal and deals with it effortlessly. Hell, he even manages to die with style — as he lays dying from his own reflected spell, he revels in the fact that the magic released by his death will mutate all of Equestria, creating the world ruled by magic he's always wanted, then dies with a smile.
The Naruto fanfic "Yakuza" makes one out of Hinata, of all people. Let me break it down for you: the Rookie 9, Team Gai, and the Sand Siblings all play a game of Yakuza, with Lee and Hinata as the yakuza. They both manipulated everyone into killing the Genin they didn't kill themselves, and at the end, Hinata betrayed Lee, causing him to kill himself in confusion, and refused to kill Naruto, leaving them the sole survivors, with Naruto taking her for ramen to celebrate. Anyone who doesn't ship Hinata with Naruto should most certainly read this.
Magnificent BitchV in a A Cure For Love. She is literally behind everything in the first arc before she is ultimatelyOut Gambitted by Light. She stole Kira's ( Higuchi's) power and she manages to fool L into thinking she is trustworthy. She integrates herself onto the Kira taskforce and L's investigation while the entire time she is in actuality the leader of Astraea, the terrorist organization that the taskforce is investigating. if not for Light and Matsuda she would have succeeded in killing L with a letter laced with sarin and if not for Misa and Rem she would have succeeded in stealing power from Kira. She is also the one who manipulated events so that Light would regain his Kira memories-this would ultimately lead to her undoing.
