The Evil Genius is the player's avatar chosen from one of three villain characters to represent your quest for world domination.
He or she has immense wealth and connections, and will use them to finance your own powerful, global-spanning, well-equipped empire to carry out your plans, referred to simply as "the evil organization". He or she will build a secret island fortress where you will repel enemy forces, command an army of skilled henchmen and loyal minions (workers, social attendants, scientists, military forces, bodyguards, etc.), and research items and evil technology (traps, interrogation devices, lasers, shrink rays, mind control devices, robots, dangerous chemicals, reanimated monsters, super-weapons, etc.) to defeat your enemies and complete your evil plans.
Your mastermind does no work themselves, but relies on minions to build rooms, operate equipment, and research objects within the base, and capture or dispatch enemy agents who infiltrate. He or she also sends minions out into the world to steal money, plan and undertake evil missions to increase your notoriety level (kidnapping, sabotage, assassination, destroying cities, etc.), steal treasures and equipment, and capture hostages that hold useful information.
To further your goals, he or she will plot to take over the criminal underworld, build your laboratory to develop evil technology and super-weapons, increase your power by raising assets in money and loot to purchase a bigger island and further cement your organization, install puppet diplomats in the world alliances to turn them against each other, and acquire the knowledge and materials needed to create the ultimate doomsday device you will use to seize power over the world.
Additional objectives involve collecting a set of special loot objects to inspire your minion forces, using a cloning machine to have fake masterminds be killed by your enemies to reduce unwanted attention, manipulate the stock market to make a large amount of money, and use several methods to permanently defeat the many super agents that interfere with your plans.
There are three Evil Geniuses to choose as your avatar for the game, with each one having special abilities and influence on your operation.
- Maximilian: A wealthy industrialist who has the ambition to control the world through advanced scientific research and technological supremacy. He didn't have the happiest of childhoods because of his stockiness and squint. Fueled by a desire to prove himself to the world, Maximilian has founded an extremely lucrative empire, but not even his riches could keep his bought friends and women from spurning him. As a result, he became bent on revenge. If he could not make the world love him, then he will have it fear him instead.
- Alexis: A beautiful heiress to a media empire with a beloved presence the world over, allowing her to command the utmost respect and loyalty from those who serve under her. Inheriting a multi-million dollar fortune and media empire from her late father, her hard work and piercing intelligence allows her business to prosper under her shrewd leadership. But years of being daddy's princess gave her a colossal ego and a constant need for adoration. Seeking a wider audience, she soon became America's darling, and eventually wanted more: more wealth, more adulation, more power. Alexis wanted the entire world.
- Shen Yu: The clandestine super-criminal with a global network of conspirators that gives him hidden influence over the governments of the world. Shen Yu was once a humble pickpocket who joined a local Triad gang and was eventually arrested by A.N.V.I.L. agents, who have implanted a communication chip inside his brain to let them spy on Triad activity. But the Triad performed even more brain surgery to reverse the wiring in the chip to access A.N.V.I.L.'s operating system. Desperate to avoid more meddling with his grey matter, Shen Yu defected and used the knowledge the chip provided to build his own criminal empire. With advance knowledge on every move A.N.V.I.L. made, he was untouchable, and soon found himself in a position to bid for world domination.
These characters are essential to the completion of their plan for world domination, and must be kept safe at all costs. If they get hurt, they can heal through the Inner Sanctum, but if they are killed, the game automatically ends. After which, you are shown a short, but interesting cutscene in which your Evil Genius is taken to a morgue, but is revealed to be a robot double with an explosive set to blow up in three seconds when his or her fake head opens, giving the player another chance to start over.
- Aura of Influence: All three Evil Geniuses radiate an aura from their person that restores the attention and loyalty of minions nearby. Alexis has the largest aura, but the slowest restoration rate. Shen Yu has the smallest aura, but the fastest restoration rate. Both Maximilian's aura size and regeneration rate are about average.
- Executions: They have the ability to execute their minions to rapidly restore all five stats to all minions who are nearby watching the execution. The amount by which the stats of the nearby minions get boosted is however different with every Evil Genius: Maximilian boosts minion stats by 5, Shen Yu boosts them by 7, and Alexis by 10.
- Taunting: Also, if you select your Evil Genius and select a cell with an agent inside, you will see a Ha Ha icon. Select this and your character will walk over and start gloating over the prisoner. This increases notoriety by 1.
- Interrogation: If your Evil Genius is standing nearby while an enemy agent is being tortured on any device, you will gain up to five notoriety points, depending on the agent being interrogated. If a Super Agent is being destroyed, your Evil Genius will make his/her way over to the interrogation scene automatically, and stand laughing uproariously while the Super Agent is gotten rid of once and for all.