Series 3
The new villain, known as Dark Oak, tries to get the Chaos Emeralds from Sonic, but Sonic scatters them across the galaxy to prevent Dark Oak from using their power. Meanwhile, six years having passed in the human world, Chris uses a portal to travel to Sonic's world, where only six months had passed, but ends up in the form of a twelve year old. During their reunion, Dark Oak and his Metarex army (similar to the Black Arms from Shadow the Hedgehog) attacks and steal the "Planet Egg" from Sonic's planet. Without the Egg, all the plants on the planet wither. Once again, Sonic and his friends venture into space to retrieve the Chaos Emeralds. Dr. Eggman follows soon afterwords with his ship: The Crimson Egg.
On the course of the Season, Sonic and his friends end up on many different planets, searching for the Chaos Emeralds and restoring life to almost barren planets. During this time, Dr. Eggman joins up with the Metarex and becomes one of the five Metarex kings soon after, along with: Pale Bay Leaf, Black Narcissus, and Yellow Zelkova. It is later revealed that Dr. Eggman was stealing technology, he, along with Decoe, and Bocoe, were later arrested by Pale Bay Leaf, and sent to jail. Sometime later, Chris shows up and tries to save him, only for Dr. Eggman to point out that he never needed any help breaking out, and the crew proceed to escape.
A few episodes later, Cosmo is eventually unveiled as an unwilling spy for the Metarex, who are part of the same race of anthropomorphic plants as Cosmo. When Dark Oak, Pale Bay Leaf, and Black Narcissus enact a plan that could destroy the galaxy, Cosmo sacrifices herself with the help of Super Sonic, Super Shadow, and Tails. Her essence is manifested in the form of a seed, which Tails plants once they return to their own planet. With the Metarex destroyed, Eggman helps Chris return to his home, implying he may never be able to return. Soon thereafter, Dr. Eggman revives his previous rivalry with Sonic, albeit a more light-hearted one.
The series ends with a couple of minor cliffhangers, such as the whereabouts of Shadow (although it is implied that Dr. Eggman knows what happened to Shadow) and what Dr. Eggman plans to do with Chris gone. It also ends showing that the seed carrying Cosmo's essence has sprouted. In the original Japanese version, Shadow the Hedgehog is still alive and he is seen placing a rose on Molly's grave.
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