Loose Ends is a Knuckles the Echidna complete story and is the first Knuckles adventure since The Final Victory. The strip appeared in Issue 101 and directly followed on from the previous issue's events.
On the Floating Island, a sense of relief at the downfall of Doctor Robotnik and the release of the Emerald Hill folk from the Biological Computer is mixed with anxiety. Doctor Zachary is believed to still be in a crater created by Knuckles during his fight against him with Sonic the Hedgehog. Urging caution, Knuckles is dismayed to find that his adversary has escaped down one of the island's many intricate tunnels. Porker Lewis suggests his likely escape route and Knuckles is about to chase him when one of the Emerald Hill folk, Sidney, stops him. The people are really grateful for being allowed to hide in the Mushroom Hill Zone, but they are fed up and want to go home. Sidney convinces Knuckles that Zachary won't be a threat for some time, so the echidna reluctantly relents.
Behind his back, the supposedly deactivated Guardian Robots have sprung back to life. Keen to protect themselves from Zachary's slaves, the civilians begin to attack their oppressors with rocks and metal boulders. The robots take offence to this action and blast them away. Knuckles is eager to stop anyone from getting hurt, so leaps between the two factions and explains that the robots won't hurt the animals. Although they worked for Zachary, it was only because of the software planted by him in their circuits. This time they were only defending themselves from the Emerald Hill attack. Defiant, Knuckles then orders the people to return to Mushroom Hill to gather their things. As they go, Knuckles enlists Porker's help in the Emerald Chamber.
Back inside, Knuckles chastises Porker slightly for having not "tidied up" the mess, but Porker didn't dare touch anything. He then points to the treasure chest that contains documents on how to repair the ailing island. With their help, Knuckles plans to return his home to its former glory and wants to enjoy this new age without the threat of Robotnik.
- Not counting Part 2 of The Final Victory, this is the first complete Knuckles story since New Master Emerald.
- Sidney is named for the first and last time. He shares a name with Sidney the Pirate, one of the Sky Pirates.
- The Guardian Robots are shown to be able to fire eye beams at targets, despite them not being charged with Chaos energy and didn't exhibit this technique against Knuckles in the previous two stories.
- Knuckles leaps in, not wanting anyone to get hurt. The previous panel showed two civilians clearly in pain.
- Zachary is mentioned for the last time in Sonic the Comic, not appearing again until In the Heat of the Night in Sonic the Comic Online.
- Several past stories are mentioned within the five pages: The Final Victory (Robotnik's defeat), Disaster! (Knuckles allowing the Emerald Hill folk to stay), Victims (the capture of the people), New Master Emerald (destruction of the Emerald Chamber) and the World Tour of Mobius all play a part.
- The Guardian Robots that attack the civilians become a vital part in Knuckles' cleanup operation.
- The closing caption stated that Knuckles would return soon, but didn't feature in another story of his own for nine more months.