In Sonic 3D Blast , Knuckles joined Sonic and Tails on their trip to Flicky Island . Having heard legends that the Flickies on the island held the key to finding the Chaos Emeralds , the group journeyed to there to find these birds. When they got there, however, the island was in pandemonium because of Dr. Robotnik who had built a base on the island from where he turned the Flickies into Badniks and used them to search for the Chaos Emeralds on the island.  As such, Knuckles helped Sonic along Tails to find the Chaos Emeralds while Sonic saved the Flickies and defeated Robotnik.
When the doctor hatched a plan involving his airship, the Egg Carrier , and the water-based Demi-God Chaos , Sonic had to team up with his friends in order to put a stop to the omelet dictator once more. While returning home through Station Square after being gone for a while on a long journey, Sonic encountered Chaos for the first time. Sonic defeated Chaos, but it escaped. The next day, Sonic saw Tails crash in his plane nearby and came to his aid. The fox took Sonic to see a plane he was working on, powered by a Chaos Emerald, but at the workshop Dr. Eggman appeared to take the Emerald. Though the duo beat Eggman, Eggman snatched the Chaos Emerald and revealed Chaos, whom he transformed into Chaos 1 with the Emerald and told his plan to make it invincible with all seven Chaos Emeralds and build Robotnikland upon Station Square. As Eggman fled, Sonic set out with Tails to get the Chaos Emeralds before Dr. Eggman. Sonic and Tails soon got two Emeralds, only for Eggman to briefly knock them out with sleeping gas and steal one. Unshaken, Sonic and Tails soon found another Chaos Emerald, but were attacked by Knuckles, who had been tricked by Eggman into believing that Sonic had at least one Emerald Shard . Sonic fought Knuckles until he dropped the Chaos Emeralds, which were then taken by Eggman and given to Chaos 2, transforming it into Chaos 4. After Sonic and the others beat it, Eggman escaped to his Egg Carrier. Sonic and Tails tried following him in the Tornado , but were shot down. ( StH : #271 ; VG : SA/SADX )