- "Unthinkable": Sonic and the Freedom Fighters have one mission: see Elias and his family leave the city safely. That'll be hard to do as Dr. Eggman attacks with his latest, most loathsome weapon to date! In such a high-stakes mission, even the unthinkable can happen. Then, in "Dark Hearts," learn the untold history between Ixis Naugus and Dr. Eggman!
Elias and his family are preparing to leave New Mobotropolis to avoid causing even more trouble than there already is, although Sonic would like them to stay. The Freedom Fighters are escorting them out of the city to the Feral Forest in the Mobo-Cruiser. Sonic is leading the ground defense with Antoine and Bunnie supporting, while Tails and Amy are providing air support. Soon after they leave they are confronted by the Death Egg and upgraded Egg Pawn designs. They easily fend them off, but Bunnie is having trouble adapting to being normal
On the Death Egg, Snively tells Eggman that they are suffering heavy losses as he himself predicted. Eggman tells him to "launch the players for act two".
They let out Metal Sonic and an upgraded, weaponized Mecha Sally. Mecha Sally easily takes out the Tornado. Sonic goes to back up Tails and Amy when he is attacked by Metal Sonic. Bunnie tries to help him but isn't strong enough and is pushed away by Metal Sonic and is knocked down by Mecha Sally. Lien-Da tells Eggman the convoy is unprotect and they have a clear shot. But the convoy has a target scramber and the all the lasers miss the Mobo-Cruiser. Eggman orders that Metal Sonic latch onto the Mobo-Cruiser and self-destruct, much to Snively and Lien-Da's dissaproval. Metal Sonic leaves it's fight with Sonic and is replaced in battle by Mecha Sally. Sonic tries to talk to her, but it fails.
Antoine goes after Metal Sonic and holds on to it and prevents it from latching on to the convoy. Eggman, learning that Metal Sonic is latched to Freedom Fighter, demand Metal Sonic be detonated right then and there. Antoine is caught in the epicenter of the explosion. The Freedom Fighter are stunned and Eggman is estatic at having finally taking out a Freedom Fighter. Much to Snively's shock, Eggman decides to leave at that moment. Despite having the Freedom Fighters on the ropes, Eggman decides that this is better than killing the former king of New Mobotropolis and that going any further would be pushing his luck. He then dismisses Snively from the deck for ruining his mood. Snively decides to wait no longer and that it's take to take the doctor down.
As the Death Egg, the Egg Pawns and Metal Sally leave, the Freedom Fighters are mourning Antoine, Elias calls to see what happened to Antoine, and Sonic tells him that Antoine made sure they could get away safely. Bunnie is hysterical, Sonic remarks that Antoine is still breathing and he takes his body and runs back to New Mobotropolis to take him to Dr. Quack.
Ixis Naugus contacts Dr. Eggman via the purple Chaos Emerald, offering information on an ideal time to attack Sonic and the remnants of the Freedom Fighters. He also asks Dr. Eggman about the time when he and Naugus met for the first time to see if he remembers, and also to check and see if their stories line up. The latter motive comes from the fact that Dr. Eggman is not Robotnik Prime.
Dr. Eggman recalls that shortly after his coup d'etat of the old Mobotropolis, he decided he would check up on the Zone of Silence to see King Maxmillian and Warlord Kodos. Upon entering the Zone in his Egg Mobile, he was captured by Feist, who was, at the time, a minion of Ixis Naugus. Ixis Naugus revealed to Dr. Eggman that Maxmillian and Kodos served him, and that Mobotropolis actually belonged to him. Ixis Naugus forced Dr. Eggman to serve him for a short while, but Dr. Eggman managed to escape by contacting Snively Robotnik from the Zone of Silence, mentioning that he could trust Snively in the early days. After escaping, Dr. Eggman instructed Snively to never again let him into the Zone of Silence.
Ixis Naugus then discloses with Eggman that Elias planned to leave New Mobotropolis with his family, escorted by the Freedom Fighters, a prime opportunity to attack them.
The story ends with Naugus bidding Dr. Eggman farewell as Geoffrey St. John enters the room, reminding Naugus of Elias' departure.
- At the part in the first story where Sonic is attacked by Metal Sonic, but Bunnie comes and tries to take down Metal Sonic but fails, Mecha Sally's eyes are miscolored red, where it originally is blue.