Knuckles lives on the Floating Island (now known as Angel Island). He lives there alone with his Great Grandfather Athair and his pet dinosaur Chomps.
When Sonic, Manic, and Sonia arrive on the Floating Island to search for their mom, they encounter Knuckles who is under the impression that the three hedgehogs are there to steal the Chaos Emerald. However, later on, Knuckles learns the truth and becomes one of Sonic's closest allies.
After some time, they see Knuckles again. Knuckles is then tricked into bringing Sonic and his siblings to Robotnik. After the big battle with Robotnik and Dingo, Knuckles returns to the Floating Island and isn't seen again for the rest of the series. Before Knuckles departs, Sonia gives him a kiss which leaves an impression that they'll have a relationship in the future.