The story opens with Dr. Eggman in his lastest lair with Orbot and Cubot. As the doctor struggles to come up with robot designs, Orbot detects a strange energy signal just outside the base. Eggman walks out to find a strange gemstone half buried in the sand. Confused, he grabs it, and is suddenly confronted by visions of Eggmanland. He drops the stone in awe, which ends the illusion, to Eggman's dismay. He takes it inside and, after spending some time testing it, finds it to be extremely useful, and begins experimenting on it. After Cubot suggests several names for the gem, Eggman decides to call it the Phantom Ruby. At that moment, the base is attacked by the Jackal Squad, a band of mercenaries lead by Infinite, who intends to sell the scavenged Eggman tech.
As the thieves attack, Eggman rages that he should have built his army up instead of studying the Phantom Ruby. At his whim, an army of Egg Pawns materialise. Confused, but deciding to go with it, Eggman orders them to attack. Infinite, wielding a sword, breaks through to Eggman. He prepares to make the finishing blow, but his blade strikes the Phantom Ruby instead, and the Jackal finds himself in a destroyed city. With Infinite distracted, Eggman knocks him away. Intrigued by Infinite, the doctor offers to hire him to be commander of his army. Though his teammates discourage him, Infinite finds the idea interesting, and admits that lately he's just been going through the motions, and finds the current world he lives in dull. He then agrees to Eggman's offer, vowing to change the world.
This story is the first piece of media to fully unveil Infinite's prior identity's face, as his prior identity was shown (but obscured) briefly in Episode Shadow.
One of Cubot's suggested names for the Phantom Ruby, the Anarchy Beryl, was previously used as the name of the Moebius version of the Chaos Emeralds from Archie Comics Pre-Super Genesis Wave comic continuity. This was further highlighted by Orbot's criticism for the name as being "too derivative". Interestingly, writer Ian Flynn, writer of this comic and the Archie Comics at the time, admitted on his Twitter that he forgot that he used the name before, making the tribute a coincidence.
Another of Cubot's suggestions was Precious Stone, which were gems used in the game, Sonic Shuffle. Like above, it was also further highlighted by Orbot's criticism for the name, in this case, that it was from the "wrong game."
The giant Eggman statue that appears in the Eggmanland illusion has the same pose as one of Dr. Eggman's artworks from Sonic Adventure 2.