The 3 months since the Death Egg War have been great for everyone, but one day, when Knuckles came back from Super Mobotropolis, he found that the Master Emerald has been broken and stolen, again. He then calls in G.U.N. to find the culprets of this heist. When Shadow and G.U.N. go to Angel Island, they find a gun belonging to criminal Nack the Weasel. They then hunted down Nack the Weasel and found him in Quartz Quadrent , but he shot down most of the G.U.N. crew assigned to get the Master Emerald pieces before they could get him. Now it would be up to Team Dark to find all the emerald pieces. Nack tells them that he has 8 shards, and he's not giving them up without a fight.
Nack and Team Dark fight, and Team Dark easily prevails. Shadow sends in a helicopter to bring Nack to jail and pick up the injured soldgers.Team Dark then splits up to find more shards. In Stardust Speedway, Shadow finds Metal Shadow, with 10 Emerald shards. Shadow then challenges Metal Shadow to a race. Shadow wins the race, but only by a few seconds. But right after the race when Shadow's taking the shards from Metal Shadow, Metal Shadow is crushed by a part of Stardust Speedway that fell on him. Without hesitation, Shadow takes the shards before he's crushed. Shadow then goes back to Angel Island to put the pieces of the Master Emerald back
The Energy Inside!Edit
Shadow and Knuckles put back together the pieces of the Master Emerald found right when Team Dark gets to Angel Island. Team Dark goes to Super Mobotropolis to see if the Knothole and Mobotropolis Freedom Fighters want to help, and they agree to helping. They go to Sandopolis and find Bark and Bean with 7 Master Emerald shards.They tell him them that they won't give them to them unless they give them something in return. The current Mobotropolis Freedom Fighters agree to letting them be with them as Freedom Fighters, so they accept. They go back to Angel Island to put the shards in. They realized they only need a few more before the Master Emerald is back together. Once the shards are back with the Master Emerald, Dimitri then appears out of nowhere on top of the Master Emerald, and uses the power of the Master Emerald to merge with Knuckles to become Enerjak, again.
Shards of the PastEdit
The Freedom Fighters are dumbfound when they see Enerjak. The Freedom Fighters try to fight Enerjak, but epiccally fail. Enerjak says that he knows where the final shards are, and he'll let them have the shards if they let him take over Mobius without a fight. Sonic agrees to the deal. Enerjak shows the Freedom Fighters where the last shards are, which somehow ended up on the courpse of a old friend, Darkness the Hedgehog. They take the shards, along with Darkness, back to Angel Island. They let Enerjak go to Super Mobotropolis. By using the Master Emerald, they revive Darkness, and free Chaos and Tikal by mistake. They then head to Super Mobotropolis to break a deal.
The Freedom Fighters, Tikal, and Chaos get to Super Mobotropolis, but Enerjak is terrorising the citizans and the Chao. This enrages Chaos to use the Chaos Emeralds to become Perfect Chaos. Enerjak finds this as a way to terrorize the city more, so he combines with Perfect Chaos to become Enerjak Chaos. Sonic, Shadow, and Darkness become their Super forms and fight Enerjak Chaos in hope to finish the fight. They fight Enerjak, and prevail. Sonic and Shadow use a new move, Chaos Drain, to drain the powers of Enerjak to turn him back to Knuckles. They then put Dimitri into the No-Zone Prizon. He says he'll be back and get revernge and bla, bla bla, bla bla!
- The Shadow V.S. Metal Shadow fight is simmilar to the battle againist Sonic and Metal Sonic in Sonic CD.