The story begins shortly after the political elections in Echidnaopolis come to an end and Benedict has been revealed to be nothing more than a machine. Knuckles and Julie-Su begin to discuss the implications of these turn of events when Knuckles spots a face in the reflection of Benedict’s head, the face of a man he hasn’t seen for nearly six years. He drops the head and runs after the figure, leaving Julie-Su behind. Knuckles is in hot pursuit of the figure, but the figure stops and turns to face his son. After all this time, father and son are finally reunited.
Knuckles tells his dad that he has a ton of questions, but Locke leads him to a place where they can talk privately. Locke takes his son to Haven. Knuckles wants to know everything that has been going, what’s happening with the Brotherhood and Haven. Slowly Locke begins to tell his son’s questions.
He starts at the beginning with a simple tale of how Steppenwolf managed to defeat a group of Overlanders lead by one Brutus Kintobor. He explains how, with the help of the fire ants reading the Overlanders’ minds, he is able to overpower them and force them off the island. They are interrupted when Knuckles and Locke touchdown in Haven. After they disembark, Locke continues the story.
He explains how Steppenwolf and Christopheles figured out that they needed help in order to protect the island, and so brought Moonwatcher into the fold. For a time, the Brotherhood was worked well, trading off jobs and each taking the turns at being Guardian of the Floating Island. However all that unfortunately came to an end when Aaron discovered an alliance between the Dark Legion and a group of Overlanders.
They were working together on a plot which would have lead to the destruction of the Floating Island. He was discovered by the legion’s current leader Menniker. Aaron tried to stop the missile, and Minniker went after him. Thanks to a slip of the tongue from Minniker when he was trying to warn Aaron about the detonator, Aaron was able to prematurely set off the device. The explosion, while saving the island, killed them both.
Locke attributed Aaron’s death to his inexperience and recklessness. It is because of this tragedy that steps were taken to insure that it would never happen again. Starting with Jordan, Aaron's younger brother, the Brotherhood instated the policy of eventually leaving the next guardian alone. Knuckles comes to realize that his father never abandoned him, but that he stayed away so that he might be better prepared for what lies ahead.
Locke then proceeds to explain a vision he had before Knuckles was born. It was a terrible vision, one that involved Knuckles facing down an unstoppable mech, with everything then ending in a flash of light, as though the world had come to an end. Locke would wake up from this vision screaming. And they kept coming, so much so that he went to his grandfather Athair for guidance. Knuckles asks he what he said. To which Locke begins to explain the genetic enhancements that he did on himself and Knuckles. However there was one final thing he had to do before Knuckles hatched from his egg.
He exposed Knuckles’ egg to the radiation of the Chaos Emerald. Afterwards, he waited with his wife for Knuckles to hatch. Locke explains how he knew that his experiments had worked. He knew the moment Knuckles was born. It was the knuckles that Knuckles has on his hands that were the first sign. He then explains how Knuckles will be their savior. After he finished, Locke suggested to Knuckles that they do something together as father and son.
- This is the series' only milestone issue. It is also the series' second single-issue story.
- There is a brief hint towards the canceled storyline Mobius: 20 Years Later when Locke is having visions of the future.
- Knuckles takes off his glove, revealing that the spikes are indeed part of his hands, something fans had wondered about for years.
- The dream showing off the future Knuckles under attack has a note stating that the Mobius: 20 Years Later universe would have been explored in a Sonic Super Special.