Evil Inc is a company, founded by Evil Atom, that provides good and services to the super-villain community. Many, but not all of the employees are super-villains themselves.

Among the central figures in the ongoing plot are Lightning Lady, Miss Match, Captain Heroic, Dr. Haynus and Dr. Muskiday.

Captain Heroic, the most prominent super-hero in the city, is secretly married to Miss Match, an Evil Inc villain who works in the plots and schemes department.

Together, they have a son, Oscar, who has exhibited no meta-powers. Oscar has not chosen to affiliate himself with either good or evil. He spends a lot of time with his father’s parents – who are also super-heroes  (Ms. Amazing and Commander Heroic) – but he attends the Evil Inc Charter School for Young Villains.

Lightning Lady entered the corporation as Evil Atom’s personal assistant. She made fast friends with Miss Match and, together, they planned to best the cocksure Dr. Muskiday at the annual Evil Inc Invention Competition. They did not win, but a bizarre chain-reaction involving the inventions of all three competitors lead to the birth of the Memo, a sentient sheet of paper that can alter its shape (by folding itself) and change the printing on its surface. Memo moves about Evil Inc in secrecy, its existence known only to Lightning Lady.

In mid-2006 Evil Atom was forced into retirement by his ex-partner Catspaw. Through his secret amassing of the majority of Evil Inc stock, Catspaw forced Evil Atom to sell his own company. Due to the intervention of the Memo, the company was sold to a group of super-hero investors fronted by Captain Heroic and the Legion of Justice.

Finding himself in a situation in which he had to find ways to make Evil Inc profitable without continuing its involvement in crime proved to be too much for the young hero. Under his tenure, the goods and services offered by Evil Inc faltered, the company’s profits margin shrunk and the Legion was facing bankruptcy due to their poor investment.

Seeing the need for a new villain to rally support for Evil Inc’s watered-down offerings, Captain Heroic started disguising himself as the Dark Hood, a villain who always seemed to succeed with Evil Inc merchandize despite their shoddy quality.

Meanwhile, Dr. Haynus – who had always wished to replace Evil Atom as the CEO of Evil Inc – hatched a plan to kidnap Commander Heroic (and, by happenstance, Oscar) to use as bait to draw Capt. Heroic in, trap him, and switch brains with him – thus becoming the CEO of Evil Inc by default.

Haynus’ evil plot was thwarted by Mr. Invincible, a Legion of Justice member, who planted explosives in the Evil Inc building. He reasoned that destroying the building would destroy the company, which had become a money drain on the Legion. If nothing else, the insurance money would refund the heroes for their disastrous investment. Cap and Miss Match were able to save the Commander and Oscar from the bomb, but the company was destroyed.

At a memorial service for  Evil Inc, Capt. Heroic announces that a lone investor has stepped in to rebuild the company: Dark Hood. Dark Hood steps forward and reveals himself to be Evil Atom. Later Cap and Evil Atom meet behind the stage and agree that, although Cap had done this favor for Evil, as of Monday they become enemies once more.

Upon his return, Evil Atom inaugurates the Ghost Board, a group of his cronies who he reconnected with at the Vulture Lodge during his retirement. They are to be placed at key positions in the company and charged with being a direct conduit to Evil Atom. Lightning Lady is promoted from personal assistant to the head of the Customer Service department.

Meanwhile, former Evil Inc manager Oculore, sensing weakness, has started a competitor to Evil Inc named Villain Zone. Villain Zone immediately begins eroding Evil Inc’s dominance in the villainous goods and services sector.

On the other side of town, Commander Heroic (Cap’s father) falls several stories to the pavement after flying up to Cap’s window. He was been getting weaker with age, Ms Amazing relates, but it’s still troubling to the Heroic family. While he’s in the hospital, he’s visited by a super-villain – later revealed to be Miss Match’s  mother – who appears to reassure the aging hero.

Through a series of flashbacks, we learn that the Commander Heroic and Miss Match’s mother, Flame, had been lovers three three years into the Commander’s marriage to Ms. Amazing. Commander had seen Flame babysitting Oscar, and the thought that Miss Match might be his daughter sent him reeling to the concrete below.

Flame’s reassurance that Miss Match is not his daughter aided his recovery, but he still moved in with Cap and Miss Match while he recovers fully.

Back at Evil Inc, a spy has been discovered who has been funneling trade secrets to Oculore, crippling Evil Inc. Iron Dragon, a villain working the Lair Acquisitions department, and who had just begun a relationship with Evil Atom’s new personal assistant, Desdemona, is a prime suspect.

The Memo and Lightning Lady, however, are following a paper trail that leads in a different direction. This, however, causes their paths to cross Dr. Haynus who assumes Memo is the spy. As they close in, Lightning Lady learns that Memo can teleport using a FAX machine. Cloning through photocopiers is hinted at as well.

The paper trail leads to Ted Jenkins, who worked under Oculore when he was a manager at Evil Inc, who had been transmitting information to Oculore through a sub-dermal implant Oculore deposited before Evil Atom fired him. Jenkins is found dead. When the police officer arrives to process the death report, a bizarre coincidence triggers a memory in Evil Atom. He remembers that Jenkins, long ago, had been a henchman for Dr. Whoosh (who is now a member of the Ghost Board). Dr. Whoosh is revealed to be the spy, and receives a promotion – a position from which he will act as a double agent, enabling him to spy on Oculore.