The Head Alien (? - 2004), was the arch-nemesis of SEMME, a member of the Alien race. The Head Alien arrived on Earth with his minions by the early 1970s, planning to conquer the Earth by acquiring Martian technology. His actions soon led to the formation of the secret government agency that became SEMME. However, after Linda Walkerton was manipulated into destroying the Martians by Dargon Chesterfield, SEMME's leadership made a deal with the Head Alien. Concerned about a possible Martian threat, they permitted him to abduct human children and infuse them with Martian DNA, creating what would become a next generation of super-powered SEMME agents.
True to form, however, the Head Alien developed his own plans for the abductees. Secretly brainwashing them, he intended to conquer the Earth at the dawn of the year 2000 (a plan he called "Year Zero"). As part of the plan, he began trying to recapture the abductees, especially Sal, whom he believed was the most powerful of all. Her (adopted, unknown to her) family began moving around at the warning of a SEMME agent. The Head Alien finally caught up with them, and killed Sal's family in front of her, forcing her on the run- she was eventually recruited by SEMME.
Later, the Head Alien was captured while torturing Joyce Brown, and was imprisoned with his thugs in SEMME headquarters. Even there, he managed to get Joyce to wipe her memories in a foolhardy attempt to purge herself of naughty thoughts. When Year Zero hit, the Head Alien was freed, and made his grand bid for conquest. However, he was forced to retreat when Walky learned that his Martian DNA let him override the Head Alien's technology and control.
Retreating to his main base, he lured Walky (and, in pursuit, Sal) there by stealing massive amounts of Nachitos. In an attempt to recruit both Sal and Walky, the Head Alien revealed they were siblings, but only succeeded in getting his base destroyed. Giving up on making the abductees into an army, the Head Alien pursued other schemes, kidnapping Ralph Zinobop to repair the Steel Duck and creating Monkey Master to attack SEMME.
During Monkey Master's attack, the Head Alien stole a Martian spacecraft, and used it to finally find the Martians' underwater city. Trying to use Sal and Walky's neuroses to steal the Martians' secrets backfired spectacularly, leading Walky to crush the Head Alien (using the stored bodies of Sal's parents). However, the city's automatic systems placed him in a Martian resurrection chamber; 10 months later, he was not only reborn, but now had enough Martian DNA in him to use their technology.
The Head Alien led a spectacular attack on SEMME, revealing their existence to the world, only to be upstaged by a deranged Sal. Escaping, he next tampered with a time-space anomaly in Canada, using it to imprison the Cheese. Once freed, the Cheese destroyed the Head Alien, but secretly, his mind became attached to the Cheese's robotic body. During the final battle with the Martians, the Head Alien assumed control of the Cheese, recreating his body (from the Anti-Head Alien) and finally having the incredible power he always wanted. Before he could truly win, the Cheese was disrupted by Alan, and the Head Alien's new body was slain- likely for the final time- by Sal.