Come Undone is the last episode of the second season of Scooby Doo Mystery Incorporated.
The episode starts with the Annunaki being in Nova speaking. It explains that the Annunaki came to Earth long ago, and made a Crystal Sarcophagus with the help of the humans. They imprisoned the Most Evil Annunaki, The Evil Entity, and all his followers. Since then, the Evil Entity has been trying to manipulate Mystery solving groups, each consisting of five members, four people and one animal. But now the time of Nibiru has come, where the nine planets will form a alignment which cause a massive gravitational disruption and will make the fabric of space and time weak, and in this point of time, the Evil Entity will be at it's greatest power. The Evil Entity wil then look to consume planets and even galaxies, but only one thing stand in it's way, Scoobert Scooby Doo.
The episode then continues after when Pericles opens the Crystal Sarcophagus in the previous episode. The Evil Entity then comes to through the Crystal Sarcophagus mouth. He suddenly grabs Scooby and explains that in order to roam the planet as flesh, Scooby must be killed and reborn to be the Evil Entity's body. But when Scooby escapes, Pericles volunteers to be the Evil Entity's body. It accepts, and Pericles absorbs the power and grows large. Pericles then exclaims that he has achieved ultimate power and that there is nothing anyone can do to stop him. But just then the Evil Entity kills Pericles, and transforms his body into a giant half-parrot and half-squid monster with horns. When Brad and Judy tell that they will follow the Evil Entity, instead of being servants the entity suddenly devours both of them. The Evil Entity then assumes control over the Kriegstaffelbots. But when Scooby attacks the Evil Entity with the Heart of the Jaguar, the weapon shatters, leaving only the staff remaining.
The Gang and Ricky Owens manage to defeat the Kriegstaffelbots. When the Evil Entity consumes Ricky Owens, it then breaks through the fire dimension, opens the crystal sarcophagus, and calls out its minions to bring the townspeople for it to consume. When everyone is consumed and only the Gang are remaining, Scooby then asks the being in Nova for help, and time stops and a blinding white light appears and Nova appears to Scooby Doo. The being then explains that the Heart of the Jagaur is not what it seems. Time then continues and the Gang are completly surrounded. The Evil Annunaki bring them to the Evil Entity and when it tries to consume the gang, it is blocked by a blue shield. The Gang escapes again. Scooby then realises that they are the Heart of the Jagaur, when they work together, their hearts become pure, and so the Evil Entity cant touch them. They also find out that the Evil Entity is drawing power from the Crystal Sarcophagus with one of his rope like structures still attached to the Sarcophagus mouth. They then run through the Evil minions, passing the staff to each other and then Scooby uses his paw to push the staff through the Crystal Sarcophagus face, smashing it. A vortex appears and sucks everything except the Gang. Then a huge explosion occurs and the Gang is landed in a normal Crystal Cove.
After a few experiences with the people near them, the Gang comes to the conclusion that by destroying the Evil Entity, they have created a new dimension where the Evil Entity never existed and there was never anyone influenced by it's evil. The Gang then promise to solve every case that they stumble upon.
- The overall mystery is solved.