Officially beginning in STC Issue 79, Knuckles went on a journey across Mobius having been stranded on the planet's surface after an encounter with the powerful alien beings known as the Tantaror. This occurred during a misadventure with the sky pirate Captain Plunder, in which Knuckles agreed to help the pirate deal with the Tantaror in exchange for a chest containing several documents relating to the Floating Island. Although the Tantaror left Mobius and Knuckles acquired the chest, he had no means of transport to return to the island.
Crossing the Channel
Knuckles' journey began at Scourge Bay, home of Mobius's pirate element. From here, Knuckles acquired a boat to cross the Mobian Channel. After two days of rowing without any wind, he found himself in dire straits. Halfway across the channel, his boat was attacked and destroyed by the mercenary Captain Claw, who wanted to collect on the bounty that Robotnik had put on the echidna's head. Knuckles fought against Claw's Octonaught mecha near a large circle of rocky pillars, which collapsed and fell on the Octonaught, crippling it. With the mecha reduced to nothing more than a rowboat, Knuckles forced Captain Claw to row them both to the other side of the channel. After making it to shore, Knuckles let Claw go and continued his journey.
Village of the Damned
Some time after reaching land, Knuckles discovered a small rural village and took lodgings in the local tavern. His sleep was interrupted by a mob of townspeople parading a young woman through the streets as they took her to be sacrificed to their Moon Goddess. Knuckles rescued the girl and they hid, but awoke to find that the girl had betrayed him to Mesmer - the leader of the cultists - in exchange for her life. The echidna was imprisoned in a spherical wooden cage and was about to be burned alive, but he knocked the cage off of the sacrificial pyre and rolled it downhill toward a stream, where it smashed against some rocks. Knuckles then attacked Mesmer and broke his staff, which released the villagers from a hypnotic trance. Knuckles questioned Mesmer, but his questions were answered by Dr. Robotnik, who had been disguised as the Green Man's landlord all along. Knuckles was tempted to kill Robotnik then and there since the doctor had no Badniks or other protection on hand, but chose to walk away rather than become a murderer.
After leaving the village, Knuckles made his way toward the Metropolis Zone. He was forced to cross the Great Mobian Prairie in order to get there, but as he crossed the wasteland he was almost killed by a herd of stampeding Apterix. He narrowly avoided death only to be captured by a group of herders and taken to the town of Backwater, where he was accused of causing the stampede. Backwater's Sherriff arrived and released Knuckles, believing that the stampede was an attempt on herder Rooster's life by Boss Krouch, who once held the monopoly on supplying Apterix meat to Metropolis. Knuckles was deputized and began investigating into Krouch's activities. He tricked Krouch into confessing putting a hit on Rooster, and then gave chase when the crooked Backwater mayor tried to flee. Krouch carried a vial containing a chemical that would drive the Apterix herd into a frenzy, causing them to stampede, and threatened to use it if Knuckles tried to bring him in. Krouch's foothold crumbled beneath him, however, and he fell into the gorge. His vial smashed and he was killed by the stampeding Apterix. In gratitude for saving his life, Rooster let Knuckles take his pterodactyl mount, giving the echidna the means to return home.
Though Knuckles now had a means to return to the Floating Island, he took a detour as he flew over the Metropolis Zone, spotting a group of protesters being assaulted by Dr. Robotnik's Troopers. He decided to intervene and fight the Badniks, and was assisted in the fight by the magician Ebony. Knuckles learned that the protest was to stop Robotnik from destroying the Fauna - sentient trees whose forest was the last still standing in the city. Omen - a sorcerer and one of Robotnik's lieutenants - arrived with a pair of armoured gorillas to arrest Ebony and destroy the forest. A fight ensued which resulted in the Great Elder Tree being blown up by a stray rocket, which angered the other trees who then began to grow to monstrous size, trapping Knuckles and co. within their forest. Knuckles pleaded with the Fauna to let them go, reminding them that they were peaceful and non-violent and that the majority of the people were trying to help them. The trees took heed of Knuckles' plea and released everyone, warning Omen and his goons never to return. After the situation was resolved, Knuckles mounted his pterodactyl again and took flight. He made another brief stop in the Emerald Hill Zone so his mount could eat, and he was approached by the Freedom Fighters who asked him to help dig out some more space so that Tekno could expand her workshop. Afterwards, Knuckles continued home to the Floating Island without further interruption. What he didn't know, however, was that the island had been attacked and Dr. Robotnik was waiting for him.