The Alien Cell is a central device to the plot of Contra Hard Corps, acting as the final boss in all routes but in different forms.
The Alien Cell was a sample of alien biomass, which was collected at the end of the Alien Wars and secured inside a military compound under the supervision of Dr. Geo Mandrake. Geo Mandrake allies himself with Colonel Bahamut, who planned to use the Alien Cell to create a weapon to take over the world. What becomes of the Alien Cell depends on the player choices during the game:
- If the player decides to pursue Deadeye Joe and Surrender and Fight Later, Bahamut will succeed in creating a weapon with the Alien Cell, which he calls Big Magnum. The player has then to fight Big Magnum, which upon being destroyed kills Bahamut and makes his space station explode.
- If the player decides to pursue Deadeye Joe and Fight to the End, the Alien Cell will get out of control and take over Bahamut's base, infesting the place and mutating the soldiers inside. After the player destroys a large mutant with a female face, they confront the Alien Cell, which mutated itself into Gomera Mosking. Upon it's destruction the infestation ends but Bahamut escapes.
- If the player decides to save the Laboratory and Surrender and Fight Later, Bahamut will use the Alien Cell to power himself up, but the Alien Cell eventually takes over his mind and mutates him into a grotesque monster.
- If the player decides to save the Laboratory and Fight to the End, after Bahamut is defeated he launches a rocket with the Alien Cell inside before dying, so the heroes pursue the rocket. The Alien Cell starts breaking free from the rocket and mutates into a blob with human faces, which is then fought as the final boss.