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!"
In the Sapphire Sea near Angel Island, Sonic the Hedgehog was diving down into the ocean because a day earlier he was thanked by the President for stopping Eggman from robbing a bank. He was then asked by the President if he could do a mission for him. After Sonic accepted, he explained that there was once an infamous pirate called Captain Seamus "Red-Eye" Macguffin that terrorized the Emerald Coast. His ship had been found and the President wanted Sonic to lead the recovery team since an energy signature similar to a Chaos Emerald had been found in the wreck and he knows the most about them outside of Eggman. If he accepted the mission he would be assisted by Chuck Thorndyke, Topaz, and Rouge the Bat, the latter eager to obtain the emerald for herself. Chris Thorndyke pointed out that they once found an emerald in the ocean but the President said they were completely different coordinates than the other ship. The President then asked Sonic if he would take the mission.
Back at sea, Sonic, Rouge and Topaz were nearby the sunken ship and were ready to go in when a shark takes interest in the trio. On Angel Island, Knuckles the Echidna saw the navy ship used for the expedition and Sonic diving underwater. He then wondered if Sonic found a Chaos Emerald, as he wouldn't go underwater for any other circumstances.
Meanwhile at Eggman's base, Dr. Eggman remarked that Sonic has fallen into his trap since he can't move so quickly underwater. He then went to his workbench and showed Decoe and Bocoe two batteries powered by rings he picked up at the bank and mentioned there was more to his plan than just the batteries. He then showed the robotic duo two new robots he'd created to defeat Sonic once and for all.
Back underwater, Sonic, Rouge and Topaz entered the ship and easily found the treasure chest of Captain Red-Eye. Before Rouge could open the chest and make off with the treasure inside, a shark attacked them by ripping its way through the ship's floor. Rouge found herself surprise but she quickly repelled the shark. Hoping for an easier target, the shark swam towards Sonic but he easily fended him off. The shark was mad by then and advanced toward Rouge and Sonic while Topaz searched for a weapon. A hand then made a candelabrum fall her way and Topaz headed towards the shark.
Meanwhile, at his base, Eggman explained to his robot lackeys that no other being could be powered up by Sonic's rings when asked why didn't he make himself stronger. It was of no matter, though, because Eggman had obtained the strongest and fiercest animals he could find to power his new robots, Komodo Dragons.
Back at the ship, Topaz used the candelabrum to intercept a bite from the shark. However it didn't seem to do anything. Topaz then waited for her fate as the shark came toward her, but the bite on the candelabrum has caused the shark to lose all of its teeth. It then fled in a hurry as Sonic explained to Chuck what happened via radio. Both Sonic and Rouge congratulated Topaz for her quick thinking and she quickly accepted before getting back to business
Above sea-level, Knuckles then saw Eggman send his two Dragonbots to attack the trio in the ship, confirming for him that there is a Chaos Emerald down there. The robots splashed into the water and threw Chuck, Tails and Chris from their life boat and into the ocean. Tails then rescued Chris while Knuckles got Chuck to safety. Eggman then told them that Sonic and his friends were now in danger, so Knuckles asked the sailors on board the navy ship for diving gear so he could go down and help them.
The Dragonbots then appeared with a crash before the underwater trio back on the ship. Sonic and Rouge dodged attacks and Rouge took the opportunity to head for the chest. Topaz then attacked a Dragonbot, only to get thrown off into some rubble. Sonic also attacked one just to get clamped up by its jaws. Rouge, seeing the trapped Topaz, left the chest to help her friend. However, she couldn't use her signature kicks to help Topaz out and she seemed doomed. Knuckles, however, arrived just in time to save her. Sonic, still entrapped, asked for some help and a ghostly figure they couldn't see said he would as he takes out the two ring batteries from a Dragonbot. Sonic then noticed one of the batteries and found two of his rings inside them, allowing himself to be powered up and help Knuckles, Rouge and Topaz to defeat the remaining robot. Eggman, with his robots defeated, then left to fight another day.
On the navy ship, the chest was revealed to have nothing but sea-shells in it, much to Rouge's disappointment. When Tails asked how Sonic beat the robot, he said he had some help. The ghost of Captain Red-Eye appeared behind the heroes and said it was the most fun he had since he'd crossed over.
Meanwhile, far off, Eggman vowed he would have revenge with his next scheme, that would use the most fierce and deadliest creatures on Earth that Sonic couldn't fight without hurting his own friends.