- By order of the President, Sonic and his friends embark on a special search and recover mission to retrieve a powerful energy source...and it just may be a Chaos Emerald! The only problem is, it is at the bottom of the ocean, and we all know water is Sonic's greatest weakness. Speaking of weaknesses, Eggman has a weakness for power, so you know he's out to get that Chaos Emerald, too!
See Sonic! Sea Battle! See Sonic Sea Battle!
One week after foiling Dr. Eggman's bank heist, Sonic the Hedgehog is visited by the President, Agent Topaz, and Rouge the Bat. The President thanks Sonic for his hard work and informs him that the ship of a notorious pirate, Captain Seamus "Red-Eye" Macguffin, has been located in the Sapphire Sea off Emerald Coast. Sonic doesn't understand why he came to tell him this, but the President explains that they believe a Chaos Emerald may be located within the sunken vessel. Chris Thorndyke tells the President that Sonic and his friends found a Chaos Emerald in the Sapphire Sea once before, but the Commander-in-Chief assures him that this is a completely different scenario.
The next day, Sonic heads underwater with Topaz and Rouge while Chuck Thorndyke, Chris and Tails act as their navigators above the water. On Angel Island, Knuckles the Echidna curiously notices Sonic diving into the water and wonders if he's found a Chaos Emerald. Meanwhile, at his fortress, Dr. Eggman gleefully watches as Sonic heads right into his trap. He explains to Decoe and Bocoe that he used the rings he stole during his bank heist to create super powered batteries that give off energy similar to that of the Chaos Emeralds. These batteries power the Dragonbots, his newest creation and the key to Sonic's downfall.
Sonic's group makes it to Captain Macguffin's ship when they are suddenly attacked by a shark. Rouge and Sonic beat the shark back, but it eventually corners them. A mysterious, shadowy figure hands Topaz a candelabrum. Confused but determined, she rushes toward the shark with her improvised weapon. Meanwhile, Dr. Eggman explains to his hench-bots that Sonic is the only living being whose power can be boosted by rings. As such, he instead drained energy from several animals to help power his robots and has decided on letting a pair of Komodo Dragons pilot the Dragonbots rather than the woodland creatures he usually uses.
Topaz rushes the shark with the candelabrum, but the fierce fish chews it to pieces. However, the shark breaks its teeth in the process and flees. Above the water's surface, Knuckles spots Eggman leading his Dragonbots into the ocean. He rushes down to help Chris, Tails and Chuck, who were thrown overboard when the Dragonbots submerged.
The robots make it into the ship and attack Sonic's group. Sonic and Topaz try to fight them off while Rouge attempts to grab the pirate's treasure. Noticing that Topaz is in danger, Rouge changes her mind and joins the fight. Knuckles lends a hand, freeing Topaz from one of the grip of a Dragonbot, but Sonic is being crushed by the other. Sonic cries out for help, and a mysterious figure removes a battery from one of the robots.
With the robot's power diminished, Sonic breaks free and finds the battery floating nearby. Two rings pop out of the battery, giving him the power he needs to help his friends finish off the Dragonbots. Eggman escapes while the crew heads to the surface with the pirate's treasure, which turns out to be a chest full of sea shells. Sonic can't shake the feeling that he was helped somehow. Behind the heroes, the ghost of Captian Red-Eye appears and muses about how much fun their underwater adventure was. Meanwhile, Eggman vows that his next scheme will be Sonic's undoing, as he will not be able to stop his robots without hurting his own friends.
- Sonic the Hedgehog
- Miles "Tails" Prower
- Knuckles the Echidna
- Rouge the Bat
- Doctor Eggman
- Christopher Thorndyke
- Chuck Thorndyke
- Seamus MacGuffin
- Amy Rose
- Cream the Rabbit
- Sonic: Dragonbots are a real drag!
- Tails: How did you beat the robot under water, Sonic?
- Sonic: I can't help feeling I had help, Tails.
- Chuck: Maybe it was the ghost of Captain Red-Eye.
- Captain Red-Eye: Aye! That be the most fun I've had since I crossed the Grand Line!
- This issue references the episode "Depths of Danger" from the Sonic X anime series. Early in production, this issue's story was intended to be a loose adaptation of that episode. This was changed when the comic was determined to be set later in the series' continuity.
- The term "MacGuffin" is used in popular culture to refer to an object that drives the plot along, which, in the case of this story, is the fitting name for Captain MacGuffin.
- Dr. Eggman makes a reference to The Wizard of Oz.
- Captain Red-Eyes mentions the "Grand Line", which is a reference to the One Piece franchise. Both the Sonic X television series and One Piece animated series had English dubs by 4Kids Entertainment that were airing concurrently when this issue was published.