The whole concept of the game is one! You start off with very little resources (a handful of Construction Minions and 50,000 dollars), and slowly go from committing petty crimes, to diabolical schemes, to world domination!
Managing to defeat any of the Super Agents, by completely humiliating them through sabotaging their plans, and besting them with your evil lair. It WILL make you truly feel like an Evil Genius, and you don’t have to deal with them for the rest of the game, INCLUDING the final Zerg Rush.
Special mention goes to the takedown of the Steele Programme, where Ms. Foxworth averts Conservation of Ninjutsu and sends waves of John and Jane Steeles at your lair, each at full strength. Fight them all off, and you've proven that the Steele Programme is worthless against you, resulting in its prompt shutdown.
Actually managing to win the game
Launching the final version of the Doomsday Device, which requires surviving a MASSIVE Zerg Rush of ALL surviving Super Agents, all Crime Lords you haven’t taken care of yet, and a whole mess of others, as everyone attempts to take you down. If you survive this tidal wave of death, you’ve truly earned the right to rule the world. The mission afterward is essentially a victory lap, where you fire the Device at all 5 Headquarters of the Forces of Justice and erase them from existence.
With the 1.12 Patch adding the ability to recruit most of the Super Agents as Henchmen, one now has the chance to dish some deliciously karmic punishment on Symmetry: after spending so much of the Campaign pilfering from your vaults, she is now condemned to watch over and guard them, able to look but never touch. In a more traditional sense, you could always execute her again using your Evil Genius the way you would normally get rid of Henchmen.
Maximilian
Red Ivan
When the world itself unites against an opposing force, that's usually it, right? Not for Red Ivan. When the Forces of Justice form P.E.A.C.E together, Ivan destabilises each nation one by one until P.E.A.C.E lays in tatters and the Forces of Justice all stand ready to go to war with each other... but since Ivan isn't ready to join in, he makes efforts to keep things just stable enough to continue with his plans unimpeded. Ivan may be a violent hothead, but under that exterior ticks a terrifying strategic mind. "The greatest general" indeed.
Right after building the third stage of H.A.V.O.C, Ivan has some special dialogue with Atomic Olga where he reveals that he was working on H.A.V.O.C while she was fighting his men. Now all the Super Soldier can do is watch as he uses it to obliterate Ivania. Red Ivan really gets one over on Atomic Olga, and seeing the horrified reaction from one of the game's most painful Super Agents is cathartic beyond belief. Not even her death elicits this kind of horror from her!
Emma
As it happens, John Steele managed to survive being shot into space in the last game. And now he's back to try and throw a wrench into the plans of another Evil Genius. So Emma decides to put an end to him. Properly. How? She captures Steele, exposes him to V.E.N.O.M gas, and then has a group of world diplomats brought to the island and killed while making him take the fall. Then, to make absolutely sure, she executes Steele personally.
Zalika
In the middle of the game, Agents start getting watches that allow them to circumvent Zalika's traps and infiltrate her base. And while Zalika can't get revenge on the watches' creator, Lina Lundstrom, she instead does the next best thing. She steals the schematics for her watches, and turns them into the V.O.I.D watches. Her machinations turn them into a must-have gadget, which she then uses to bring everyone under V.O.I.D's control. Lina Lundstrom created a gadget that was supposed to help bring Zalika down, but the latter was smart enough to turn it into something that condemned the whole world to her control. Nice going.
