After gaining the seventh and final Chaos Emerald from Shadow, his old programming activated. With that, Shadow used the keywords created by Gerald Robotnik to deactivate Emerl's programming: "Bring hope to humanity". With those words, Emerl becomes his old self. Shadow asks Emerl to battle him one last time, of which, Shadow emerges victorious. After the battle, Emerl asks to see Sonic and the others. Shadow then replies that he'll battle Emerl again once he beats everyone. After beating Sonic, Sonic says that he was holding back and the Gizoid returns to Shadow to fight him in combat. Emerl wins. After beating Shadow, Sonic appears and teams up with Shadow, thinking that Shadow wouldn't give Emerl a big enough challenge on his own. Emerl then battles the two hedgehogs and wins. The Gizoid then thanks Sonic for helping and protecting him and thanks Shadow for helping him discover who he truly is. But, not long after, Dr. Eggman appears and tells Sonic and Emerl about the Final Egg Blaster. Sonic then proposed that Emerl should go to stop Eggman, since he reactivated Emerl in the first place.
After traveling to the Death Egg and beating Eggman, Emerl turns his back to leave but Eggman activates the Final Egg Blaster, destroying a group of stars. Upon seeing this massive display of power, Emerl's programming activated: "if the Gizoid sees overwhelming power, he'll break his Link with his former Master and form a new Link with the owner of that power". This is what Eggman wanted, but it worked far too well. Emerl then pointed the Final Egg Blaster at Earth with plans to destroy it. Eggman, not wanting the world to be destroyed (then he wouldn't have anything to rule over), tried to stop Emerl, but the Gizoid merely knocked him out. Sonic and the others see this and try to think of a way to stop Emerl. It was then decided that Sonic would use the Master Emerald's power to negate the Chaos Emeralds inside of Emerl. When Sonic attempted to use the Master Emerald's power, Emerl got annoyed by its light and shattered it. Tails then came up with another solution: if Emerl takes enough damage, he'll return back to normal, but he'll probably be destroyed as well. Sonic, seeing that there was no other option, fought Ultimate Emerl in a 10 round, 30 second fight (the Final Egg Blaster fires in 30 seconds).
After the fight, Sonic proposes that Emerl returns home and have some fun, like tricking Knuckles into doing something stupid, but Emerl simply said that he was going to miss everyone and disappeared in a flash of white light, leaving behind a shard of the Chaos Emerald.
- The only thing different about Ultimate Emerl's appearance is that the "eye" on his forehead opens, revealing a blue eye panel and black "pupil".
- After gaining the last Emerald, Emerl's "eye" is still closed during his side views. Only during his front views is his "eye" open.
- Typically through Tails' Virtual Training (though there's a chance they can be unlocked through normal gameplay as well), Emerl can pick up moves from Ultimate Emerl. However, he doesn't have enough Skill Points to equip them all, being capped at 500 and the necessary amount of points to equip all his moves being 690.
- In the game, if you pick his ULT. fighting pose, his eyes change to a light purple color.
- Speaking of this, in the game his moves are faster, over-powered versions derived from Sonic's Moves with aftereffects of Tails, Knuckles, Rouge, Amy, Shadow, Chaos, Cream and Gamma' Moves.