While the Alpha Gang take down the Gel Jarks with salt, Rex and Zoe intercept Seth, and Max catches up. Suddenly, the Space Pirates' ship slams out-of-control into the Backlander, and Seth drops all the Cosmos Stones! Rod and Laura go to retrieve the Cosmos Stones, while Max's Dino Bracer strangely repells the Black Cosmos Stone. Seth nearly defeats Ace and Paris, but Chomp takes down Cryolophosaurus with Dr. Z's new move: Final Thunder.
Rod and Laura get all the Cosmos Stones, but the Black Cosmos Stone, Seth, and the card of the beaten Cryolophosaurus have disappeared. Seth had left with the Stone in an escape pod and left a rolled-up Gel Jark behind.
Spectre contacts the D-Team and offers to trade the other Cosmos Stones for their parents and they accept, but when their ships dock to make the trade, the parents refuse to let it happen. Dr. Cretacia throws a paper airplane to them and Dr. Ancient orders Jonathan to leave immediately. Jonathan obeys and leaves, and with broken engines, the Space Pirates couldn't follow. The D-Team realize the paper airplane is actually Max' mothers' recipe for milkshakes, Zoe's mom's recipe for apple pie and Dr. Creatacia's recipe for cookies.
Jonathan then finds something shocking. Back in the present, Seth has appeared at the D-Lab and captured Reese, Dr. Owen, and Patrick with Cryolophosaurus! Seth contacts the Backlander and tells them the only way to save their friends is to hand over the 6 Cosmos Stones. As they head to the present, the Pterosaur tries to stop them, telling them that having all the Cosmos Stones in the same time is too dangerous, but they are being sucked into the time portal and are unable to steer away. The Backlander crashed through the Pterosaur and enters the present.
Upon arrival, they teleport down with all their dinosaurs to confront Seth, who activates the Gel Jark pod still on the ship. He tells that instead of just destroying the Universe, the fusing of the 7 Cosmos Stones would start up another Universe in its place, one that he would rule. Then the Gel Jark, having knocked out Jonathan with a lightning rod, teleports down with the Cosmos Stones, letting the Backlander crash.
Then Seth has Cryolophosaurus attack, knocking out Chomp, Ace, Paris, Terry, Spiny and Tank with Snow Crystal. Seth then heads into the D-Lab, pursued by Dr. Z and Helga. Just then the Space Pirates arrive and attack, defeating all of the D-Team's and Alpha Gang's dinos. A blast from Armatus' Spectral Stinger also destroys the D-Lab.
Spectre then grabs the 7 Cosmos Stones with a beam and merges them, forming the Dark Pterosaur. He makes it charge up Gigas, Armatus, Maximus, and Brontikens with extra power. Spectre trys to absorb the energy from the Dark Pterosaur into his ship, but it encompasses the ship, increasing monumentally in size in the process! The end of the Universe and all of Time-space is nearing . . .
Seth/Cryolophosaurus vs. Max/Chomp
Chomp attacks Cryolophosaurus, but it dodges, so Chomp uses Ultimate Thunder. However, Cryolophosaurus dodges it and attacks again, knocking Chomp back. Cryolophosaurus uses Snow Crystal, and Max recalls Chomp just before the attack hits.
Seth/Cryolophosaurus vs. D-Team
Rex summons Ace, Zoe summons Paris, and Element Boosters are applied. Paris attacks, but Cryolophosaurus knocks her back. Then Ace knocks Cryolophosaurus over. Max re-enters the battle with Chomp summoned and armored.
After a short interruption of the Space Pirates crashing into the Backlander, Cryolophosaurus uses Blizzard Smash and nearly freezes Ace and Paris, though still hitting them hard. Chomp attacks Cryolophosaurus, but it dodges and throws him back. Dr. Z runs up and gives Max the Final Thunder Move Card, which he uses to defeat Cryolophosaurus, but Seth reclaims its card.
Seth vs. D-Team/Alpha Gang
Cryolophosaurus uses Snow Crystal and knocks out their dinos, but doesn't defeat them. Then the Spectral Space Pirates arrive.
D-Team/Alpha Gang vs. Spectral Space Pirates
The Space Pirates teleport down with their dinos.
Spectral Space Pirates win
(the parents aren't willing to be traded to the D-Team for the Cosmos Stones)
-Spectre: "Hello, they're trying to free you here. Why don't you just say 'thank you'?"
-Sheer: Spectral Punisher!
-Gavro: With the side of Spectral Lancer!
-Foolscap: And for desert, Spectral Stinger!
-Rod & Laura: Grandpa, no!
-Ursula, Zander & Ed: Dr. Z!
-Zoe: The Cosmos Stones!
-Max: He's merges it, them!
-Zoe: Don't do it!
-Rex: It too dangerous!