- Shadow's episode features him willingly relinquishing his Chaos Emerald—the only one that hasn't been absorbed by Emerl—in order to awaken Emerl and complete his evolution as the Gizoid. When Rouge expresses concern over this, Shadow replies, "It's okay. I have Maria in my heart."
- The ending. After spending the entire game learning, forming strong friendships, and growing more powerful, with the player essentially watching Emerl grow from babyhood to a mature young robot, you play as Sonic to kill him once he goes crazy.
- Tails' speech at the end. "Maybe one day... if the world finally knows true peace... if this world no longer needs weapons or wars... if we can make this world a truly peaceful place when we're older... if we can make a world where there's only laughter... Do you think we'll be able to play with Emerl again?"
- As flanderized as Amy is in this game, she still cares deeply for Emerl; he calls her "Mom" in return. This makes the ending hit harder.
- Emerl thanking everyone at the end of Shadow's chapter, saying that when he was with Sonic and friends, despite their fighting he didn't feel worried. He felt fun, excitement, and happiness.
- After you beat Eggman, Emerl thanks him for waking him up and tries to make him promise not to do anything bad. Instead, the doctor overloads Emerl and makes him go power-mad.
- Before the final boss fight, an overloaded Emerl is in severe pain and calls out to Sonic and Shadow for help, and Amy as his Mom.
Emerl: Power... Overflowing... Can't hold it in... Can't hold it in... Sonic... Shadow... Help... In such pain... Mom... It hurts... The pain...