Knuckles was first thought to be an enemy of the freedom fighters because when Robotnik crash-landed his death-egg he landed on the floating island and met knuckles, he then told knuckles that an evil hedgehog called sonic was going to come to the island and steal the master emerald. So when sonic came looking for Robotnik on the floating island he met knuckles who believed he was an enemy and set up many traps for sonic until they had a fight in the sky sanctuary zone and as sonic won knuckles witnessed Robotnik stealing the master emerald and realised who the enemy was and so did sonic. So sonic had already retrieved the other emeralds and so turned into super sonic and flew after the death-egg which Robotnik was re-launching with the combined efforts of sonic and knuckles the death-egg was destroyed. Knuckles was so eager to talk to Robotnik because he is the LONE guardian of the floating island and nearly the last trace of the ancient echidna race.