Sonic faces off against Dark Oak once again, Eggman has taken control of Blue Typhoon and outside the fortress are Metarex armada led by Red Pine. The situation can't seem to get any more dire when Red Pine and his crew begin to attack their own base.
To complete his final revenge, Dr. Robotnik's revenge was to crash ARK into earth, destroying everything and everyone. Sonic must now convince Shadow to help save the world from destruction.
With the sacrifice of Cosmo, Dark Oak has finally been destroyed. The crew mourns the loss of Cosmo though they are quickly faced with another trouble as the Planet Egg begins to release its explosive energy.
Shadow breaches Blue Typhoon, appearing in Cosmo's room. As he knocks Sonic and Chris unconscious, Shadow goes after Cosmo whom Tails has taken away to safety.
As Shadow tries to recall who Sonic and his friends when a Metarex named Scarship arrives to complete its newly assigned mission: to destroy Sonic and Dr. Eggman.
As Amy wonders about fate of Shadow and the rest of the crew begin to fix things up around Blue Typhoon, they come across a Chaotix ship who had been drifting in space since they last made their delivery to Chris.
With everyone back in their home worlds the crisis has been averted and all seems to be back to normal. Except, no one seems to know where Sonic is. His friends and even Eggman begins to wonder where the blue hedgehog might be.