When the attack key is pressed, a ball is dropped in front of the user. This ball will automatically explode if left alone for three seconds, but it can be rolled around by moving into it, resetting the countdown each time it moves. It will explode upon contact with enemies as well. Pressing the attack key again while next to the ball will make the user kick it, causing it to fly at an upward angle while piercing through exposed enemies and bouncing off of terrain up to nine times. The kick itself does no damage, and holding the up key before kicking the ball will raise the angle it travels at. Setting a Mega Ball onto a Spring or Bouncy Ball will cause it to bounce up at the maximum height they allow indefinitely.
Mega Ball can also be used to boost jumps by holding the jump key while touching it. With proper timing, it can be used for infinite midair jumps, as long as weapon energy remains. Only one Mega Ball can be present at a time, and it can be used twenty times with a full energy gauge. In a change from the original, the ball can now be placed on spikes. Both forms of the weapon are incapable of destroying Dust Blocks and Ice Blocks, but can destroy Pole Eggs if dropped from above.
- Mega Ball is unique in that it's a Special Weapon that is not obtained by defeating a Robot Master, instead being gifted by Dr. Light. It shares this trait with Magnet Beam.
- If the player drops a Mega Ball onto spikes, then attempts to boost jump off of it after falling at a height of five tiles or greater, they will instead die from touching the spikes.