Eggman has a Chaos Emerald that he puts into Chaos so Knuckles can be a 'guinea pig' to his latest plan. Upon finding 6 Master Emerald shards (three from SPEED HIGHWAY and three from CASINOPOLIS), Dr. He heads to STATION SQUARE and makes that a starting point for his own journey. He comments on the sight, but now he knows what to do: find all 15 pieces of the Master Emerald before things get worse.

When Chaos is awoken out of the Master Emerald, Knuckles tries to get an even battle out of Chaos, but Chaos escapes due to Eggman's attempts. He doesn't know why he's been given this job in the first place (why it was his fate overall), other than to be destined to live here forever. As far back as the Guardian of Angel Island can remember, he has been living on the dark island, always guarding the Master Emerald from anything that could harm it.