The Intelligencia was formed by the Leader. He recruited some of the greatest criminal minds on Earth for one purpose: recollect the lost information of the Library of Alexandria. He first got the Wizard to join, followed by Egghead, the Mad Thinker and the Red Ghost. In order to safeguard the information, they got the cooperation of Doctor Doom.
Together they created a device that made them fall slightly out of time with the real world, making them undetectable to even the greatest of technologies. The device was powered by their combined mental capabilities (Doctor Doom excluded). Their first heist was a success, stealing one third of the information from the Eternals.
Over the years the team continued to plan for their future heist while at the same time endeavoring on solo missions. They often assisted each other in prison breaks, all the while keeping their alliances secret. They were also responsible for resurrecting and reforming the Absorbing Man, Sandman and Klaw on multiple occasions in order to keep them unaffiliated with one another. When Egghead was killed, they needed a replacement to make their machine work. The Leader chose MODOK.
They stole the next piece of information from Wakanda, a remarkable feat considering the nations advanced technology. With this information, Doom built a tachyon beam that inadvertently caught the attention of the being known as the Beyonder. After these events, the team did smaller missions to obtain further information.
The final piece of information was located in the Library of Atlantis, the team luckily retrieving it before it's destruction. Upon return to Latveria with the info, they were betrayed by Doom, who stole it all. The team disbanded after the Leader left the battle with Doom, knowing they could not hope to beat Doom in his own land.
Years later, the Leader was approached by MODOK, who had some interesting information. With info he had learned from the texts, MODOK used gamma and cosmic radiation to create the Red Hulk, who could be used to stop the Hulk. They also needed to take out the opposition, which was the eight greatest minds on Earth besides their own. This also included revenge on Doom.
With MODOK's technology, the Leader also created the Red She-Hulk. With a blood sample from Abomination, they also transformed Rick Jones into the A-Bomb and planned to use him against his friend the Hulk. The Red Hulk drew up a battle plan for the Intelligencia, but was cast out of the group. Now seemingly allied with Lyra and Doc Samson, the Intelligencia made their first move. They successfully capture Reed Richards (sending the Wizard and his Frightful Four) and Doctor Doom (sending the Cosmic Hulk robot).
The Red She-Hulk is then sent to capture Hank Pym, who she captures with the same mentally reducing technology used to capture Doom. The Red Ghost is then sent to capture the Black Panther, but gets a two for one and captures the Beast as well. They were all brought aboard the Golden Hellicarrier, which the team took over and made their own base.
Bruce Banner and the Red Hulk began to work together to stop the Intelligencia's plot. But the whole time, the Leader and MODOK watched their foes and planned accordingly. When the Hulks, the Fantastic Four, the X-Men and the Avengers attacked, it all fell into their schemes. With the Red Hulk captured, they used him to create many other red Hulks out of AIM agents and turned their other foes into super-powered Hulks as well, setting the stage for World War Hulks.
However, despite their intelligence and their power levels, the Intelligencia were unable to match the mind of Bruce Banner who was able to see through their illusions and used his knowledge to use their equipment to re-absorb the gamma radiation in all the hulks and transformed back into the Hulk but with a combination of the Professor Hulk and the Sakaar Hulk. The Leader and M.O.D.O.K were defeated and the rest of the members of the Intelligencia fled but were later captured by Jen Walters and the Savage She-hulk.
The group later escaped and came into possession of a deceased Space Knight, intending to reverse engineer his technology for their own plans. They also kidnapped Spider-Woman when she was caught spying on their plans. The subsequent battle with the Avengers (who came to rescue Spider-Woman) ended with the revelation that the Space Knight "corpse" was actually a disguised Ultron, who had now returned to Earth to conquer the planet.