Big Magnum is a secret weapon powered by the alien cell and is piloted by Colonel Bahamut at the top of a really long elevator inside a station in space. It is fought at the end of the game if the player selects the following options:
- "Go after Deadeye Joe"
- "Surrender and fight later"
It is a huge mechanical device featuring a glass capsule containing the aforementioned cell, a huge alien head monstrosity connected by several tubes throughout its brain. It counts with a highly articulated mechanical arm with a powerful plasma cannon mounted at the end. This cannon also happens to be the only part where the boss can be damaged. As the boss sustains damage, the cell will start melting, looking even more grotesque.
The cannon has several modes of attack. It fires single blasts out of its main gun, as well as a few shots that hover above the player before falling straight down. It also launches a floating blast that streams beams out of it in three directions while turning clockwise, forcing the player to run around the walls and ceiling while taking shots at the boss in order to survive. In certain occasions, it may even release powerups for the player to collect.
Once Big Magnum is destroyed, the base will explode killing everyone on board... including the player. A posthumous message follows in the end credits honoring their ultimate sacrifice.