Prior to the timeline being altered by King Sonic, Dr. Eggman still suffered defeat. With his empire crumbling around him, Eggman sought out help from Dimitri, who was immobilized and on life support. When Dimitri refused to help him, the enraged Eggman ripped him from his life support unit, thus resulting in Dimitri needing his head to be removed from his body and preserved in a glass ball. Some time following this, Eggman stole the Master Emerald, causing Knuckles to transform into Chaos Knuckles once again. With his new powers, Chaos Knuckles killed Dr. Eggman.
Following the timeline's alteration, Dr. Eggman's fate is unknown, though the planet was conquered by King Shadow after the Second Robotnik War.
- Eggman presumably perished at the end of the Second Robotnik War, as Sonic seemingly disappeared at that point as well (due to him making changes to the timeline). It is possible he survived the battle and was eventually overthrown by Shadow the Hedgehog, but his actual fate is unknown.