The Morph Ball is a fundamental ability, allowing Samus to transform into a compact sphere for navigating tight spaces. Several upgrades enhance its capabilities. The Morph Ball Bomb allows Samus to deploy small bombs, destroying weak blocks and activating Morph Ball slots. The Boost Ball provides a burst of speed, useful for traversing half-pipes and breaking through certain obstacles.

The Spider Ball allows Samus to adhere to and traverse magnetic tracks, opening up vertical and inverted pathways. These upgrades are essential for reaching new areas, solving environmental puzzles, and finding hidden collectibles. Mastering Morph Ball movement and its various upgrades is a core aspect of Metroid Prime 2's gameplay.