Knuckles is pouting about failing his duty of guarding the Master Emerald and that he only has nine pieces. He thinks he failed his duty, but then sees another vision of the past where the shrine is covered with flames and a worried Tikal looking on. He then realizes that feeling sorry for himself won't help, and he continues his search.
Inside the Egg Carrier, Amy is in a dungeon with Lily and calls to Eggman to let her out, but it doesn't do any good. She was upset that Eggman had to spoil a nice gourmet meal she was going to make for Sonic. She then remembers a time chasing after him when she's suddenly attacked by an E-12 Behemoth, but Sonic destroyed it and saved her. She then said to Lily that Sonic would come to save them. Elsewhere on the carrier, Eggman gives orders to Gamma, Delta, Epsilon, and Zeta to find and capture Froggy, who's been driven insane by Chaos' tail and has eaten a Yellow Chaos Emerald. They all leave to find a frog with a tail.
Meanwhile, Knuckles finds the keys to an abandoned Ziggurat called "The Lost World", and finds 3 more pieces of the Master Emerald and is sent back into the past again to Tikal, a group of Chao and the Master Emerald shrine. The Chao lead her to the top of the shrine and show her the seven Chaos Emeralds and the Master Emerald, and she realizes that the Master Emerald is the controller that unifies the Chaos. Knuckles is then sent back to the present time in front of the shrine. He then puts together the Master Emerald pieces he gathered and the Emerald is almost complete. There's only last three pieces left. The Master Emerald then shows Knuckles an image of the Egg Carrier.
Meanwhile, Chris and Big are still looking for Froggy in the Emerald Coast, when Chris spots the X Tornado flying overhead and wonders if Tails is okay. Gamma, Delta, Epsilon and Zeta are still searching for Froggy, and they are near where Chris and Big are. Delta, Epsilon, and Zeta all find frogs with no tails, but Gamma spots Froggy after Chris and Big find him. Big turns to go home, but Gamma grabs the crazed frog from Big and heads back, with the worried feline pleading behind. Gamma is about to return when a blinding flash takes him back in time. He tries to figure his location, but it doesn't work. He heads to the alter and lowers his cannon at the presence of the Chao. Tikal rushes to their aid, but she realizes Gamma's not part of the Knuckles clan and gives him some helpful information about the Chaos Emeralds, the Chao and their draconic protector, Chaos, before Gamma reverts to his time. Knuckles has no idea where the fortress is. As he walks across the bridge, he spots Gamma heading to the jungle. He decides to follow the rogue to the jungle and into the fortress, which takes off. Chris and Big go after Gamma on to the Egg Carrier.
During the flight, Tails meets up with Sonic at the peak of Red Mountain and takes off in the Tornado-1, powered by a Red Chaos Emerald to go after the Egg Carrier to save Amy. Sonic tells Tails that he shouldn't try to take Eggman on while still recovering, and that he should do it alone. Tails reminds Sonic that the two of them together are a team and it will be easier if they both look together. Gamma and his brothers argue over whose frog is the one, but stop when Eggman walks in. When Eggman sees the frogs with no tails he gets enraged at his robots, telling them that the frog he wants is crazed, has Chaos's tail and even ate a Yellow Chaos Emerald... but settles when he sees Froggy in Gamma's hand and is delighted that Gamma succeeded. He proudly congratulates Gamma for his capture and dismisses Delta, Epsilon and Zeta for their idiotic failure. Eggman then tells Gamma to find the bird named Lily with Amy, then departs. He walks into the wrong room and sees Beta being repaired and upgraded. This somehow upsets him. When he reaches Amy's cell, she refuses to give up Lily and asks him why he wants Lily. Gamma simply responds that he must obey the Doctor's orders. Amy persistently ignores his orders and tells him that love isn't part of his programing, which Gamma angrily replies that she knows that she shouldn't know. Lily flies out of the jail cell and looks Gamma in the eyes. Gamma then tells them to escape and deactivates the cell. He tells them it is dangerous and that they'll be at the Mystic Ruins base soon.
Despite stormy weather, Sonic and Tails find Knuckles on the Egg Carrier and he joins them onboard. A battle then ensues between the Egg Carrier and the Tornado 1. Tails then springs a surprise on Eggman and transforms the Tornado 1 into the Hyper Tornado. Tails manages to destroy any missles being fired and disables the Egg Cannon and brings the Hyper Tornado close enough to land. Sonic tells Tails to bring it in for a smooth landing, but Tails says that they'll have to settle for nice and bumpy as he forgot that the Hyper Tornado has no landing gear and Chuck installed the water landing button. The engines stopped, the airbags went off, and the siren went off. Sonic and Knuckles both exclaim, "WHAT?!?!" and the Hyper Tornado crash lands on the Egg Carrier.