During this battle, the player is basically playing a game of dodgeball against Eggman, who is piloting the Egg Pinball. Eggman is below the player, moving back and forth, launching blue crystal balls at the player, which ricochet when they make contact with a wall. The platforms on the sides of the arena will fall into a bottomless pit if stood upon for too long.
To beat this boss, the player must successfully knock Eggman's balls back at him by jumping into or attacking them (turning them orange). As Eggman takes more hits, he will fire more frequently, which can become chaotic as the balls move faster. Gemerl is just above Eggman's cockpit.
Once the machine is hit with eight balls (six on Easy mode), the Egg Pinball goes down, and the player can move on to Chaos Angel.
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References
↑Flynn, Ian; Sega (8 December 2021). "Sonic Advance 3". Sonic the Hedgehog Encyclo-speed-ia. Dark Horse Books. p. 145. ISBN 978-1506719276. "Bosses: Gemerl and Egg Pinball. Gemerl fights faster and fiercer, shrugging off blows with a new shield ability. Dr. Eggman later launches ricocheting projectiles from his mobile turret. Hit them back at him to deal damage."