The Mega Core-X (also known by various other names: Giant Core-X, Varia Core-X, or Barrier Core-X) is the X that steals the Varia Suit from NOC's Data Room before Samus is able to download it. This special Core-X massively grows in size and gains peripheral Core-X as an effect of downloading the Varia Suit. After witnessing this X download data, Adam comes to the conclusion that the X can process data organically, much like Mother Brain, the Aurora Units, or Security Robot B.O.X..
The Mega Core-X can only damage Samus by ramming into her, a simple, but dangerously effective means of attack considering its large size makes it difficult for Samus to dodge. To add to the complexity of the situation, there is a pool of water below during the battle, and falling into it will make Samus very vulnerable to attack because she lacks the Gravity Suit, meaning her movements will be sluggish.
When Samus battles the behemoth, she is unable to use Missiles against its large form, an immunity granted by the Varia Suit to the X. She can, however, attack it with the Charge Beam. Samus can destroy the smaller Core-X around the creature, leaving it more exposed to her shots. After damaging it enough, Mega Core-X will diminish back to its original, Core-X state. It will then be susceptible to Samus's missiles, allowing her to break its shell and absorb the Varia Suit she failed to retrieve earlier.
- "How did that X download the Varia Suit data? This doesn't seem to make any sense at all, unless the X... Unless the X have the ability to process data organically..." —Adam Malkovich (Metroid Fusion)