Fresh from his last adventure with Tails in the Nameless Zone and after a hard day's work repairing the Emerald Chamber, Knuckles is tired and about to retire to bed when the alarm system sounds. Dubious as to whether there is an intruder on the Floating Island, or just dust in the works, Knuckles goes to check anyway. Travelling through the 'mysterious' Zoom Tube, he arrives in Megopolis City, the capital before the rest of the echidna race disappeared. Suddenly, Knuckles hears a noise and rounds a corner to find a robot (later discovered to be a Guardian Robot) digging in the rubble of the Zone. Acknowledging its obvious power, Knuckles calls to it, but the robot's reply is to fire its machine gun in the echidna's direction. Trying the direct approach by punching it, the robot punches back. Knuckles seems to find the robot familiar, but can't dwell on it, so he punches the ground, creating a fissure which the robot falls into. Wondering what the robot was looking for, Knuckles hears a voice from the rubble. Bewildered that masonry could be talking, a white echidna emerges from the pile of rocks. Calling himself Doctor Zachary, he announces himself as one of Knuckles' race, the first to return.
Knuckles takes Zachary to see the Chaos Emeralds, amazed that something so small can keep an entire island afloat. Knuckles has many unanswered questions about why his species left the island, but the 'doctor' is tired, weary from running from the robot. Knuckles says he has dealt with it, but Zachary isn't so sure, warning him that it is virtually indestructible and won't rest until it has caught him. Later, Knuckles searches ancient documents of the island and finds that the robot was built by his people. Unsure why one of those would attack Zachary, he goes to show him the scroll. On the way, however, the robot bursts through a wall and begins to attack Knuckles again. Zachary is awoken by the noise and freezes in fear when he sees the robot. Knuckles, distracted by Zachary's plight, is knocked out cold by the robot. When he wakes, Zachary warns that the robot went straight to the Emerald Chamber. As the island shakes, the echidnas arrive to see the robot smash the Master Emerald into pieces.
Having destroyed the biggest Emerald, the robot moves on to others. Realising the robot is absorbing the Chaos energy, Knuckles leaps at it, against Zachary's advice. The robot sees him and charges a green eye beam, firing it at Knuckles. Zachary presumes Knuckles is dead and reveals his true alignment, that it was all a trick all along. Zachary removes a seal on his chest and places it on the robot, causing the head to open. As he climbs in, he reveals he wants to 'take his revenge' on Knuckles' lost people, but wants to warm up by killing the people of Mobius. As he bursts out of the island, Knuckles follows through a zoom tube and rips off a wing of the robot, rending it flightless. As Zachary commands the robot to kill Knuckles, Knuckles spots a mountain and realises that the island is falling fast, right into a Mobian mountain range.
As the island hits the mountain, a massive quake rips through the island, toppling many houses in the Mushroom Hill Zone. The shaking stops as suddenly as it starts, with Knuckles realising they must be stuck on top of the mountain. Zachary proclaims that he will Knuckles before he dies with the rest of the island. The robot attacks but Knuckles responds buy throwing a rock at it, decapitating the robot. Unprotected, Zachary pleads with Knuckles not to hurt "an old echidna". However, a minor tremor hits the island and the area that Zachary is standing on collapses, taking Zachary and the robot with it. Knuckles wants to stay on the island until the end but sees the robot's head and has an idea. Back in the Emerald Chamber, Knuckles put the head with the other Emeralds and the island begins to rise! With everyone safe, Knuckles knows that next time an echidna show up, he'll be asking a lot more questions.
- The first shot of Megapolis City shows a version of Tikal (not to be confused with the character), an ancient Mayan building. This building would reappear, in a very similar style, in the video game Sonic Adventure.
- Page 3's lettering and speech bubbles are blue.
- Zachary calls the ancient echidnas "Knuckles' lost people", suggesting they are not the same as his ancestors.
- Zachary's death was possibly the first time we see a Mobian character die. This is rectified in Victims, where we learn how Zachary survived (barely).
- Knuckles states that the next time he meets another echidna, he will ask more questions. This happens to be in Sonic the Comic Online, where he meets Tikal. However, her memory is erased, ending all possibilities of answers.