While Sonic and Tails pursue the Egg Carrier, Knuckles heads deep into the Mystic Ruins Jungle. There, he finds a pair of Fighting Gloves, a pair of field emblems, and a pair of mysterious statues that open the path to a Lost World. At the same time, Big the Cat returns to his home in the jungle to pick up his Power Rod and a new fishing lure to enhance his fishing skills. Then the feline heads to the Ice Cap Zone, where he finds the very useful Life Belt, which makes fishing significantly easier.
High above, the Tornado is shot down by a huge laser blast from Eggman's massive vessel, and Sonic is sent flying back to the Emerald Coast while Tails crash-lands elsewhere. Worried about Tails' safety, Sonic looks frantically for the young fox and his downed aircraft, but finds Amy Rose instead. As it turns out, a small Flicky escaped from the Egg Carrier during the battle, literally crashing into Amy. Unfortunately, the bird is being hunted down by another of Eggman's robots, and Amy needs Sonic's help to protect him. At Amy's insistence, the two hedgehogs run into Twinkle Park to escape the robot.
Having found more shards of the Master Emerald, Knuckles is shown another strange vision from the past. When the vision ends, Knuckles is returned to the alter and attempts to restore the Master Emerald only to discover a few pieces are still missing. A vision of the Egg Carrier appears inside the Emerald, leading Knuckles to believe the remaining pieces are somehow on the ship. After spotting E-102 Gamma, still on his hunt for the tailed frog, Knuckles decides to give chase, hoping the unsuspecting robot will lead him straight to Eggman's base and then to the Egg Carrier.
While Sonic had been ejected from the Tornado following the battle with the Egg Carrier, Tails tried desperately to save his craft but crash landed back at the Mystic Ruins. After regaining consciousness, Tails determines that he needs to finish his prototype aircraft and realizes a new Chaos Emerald is needed to get it working again. A quick search in the jungle and Tails finds the Red Chaos Emerald, but a certain tailed frog grabs the gem and heads down a sandy cave with the fox in pursuit...
