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 repels the Black Cosmos Stone. Seth nearly defeats Ace and Paris, but Chomp takes down Cryolophosaurus with Dr. Z's new move: Final Thunder. However, Seth reclaims his card and takes the Black Cosmos Stone.
Rod and Laura get all the other Cosmos Stones. 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 can'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 crashes 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 down all 6 dinosaurs with Snow Crystal. Seth then rushes 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 wrecks the D-Lab.
Spectre then grabs the 7 Cosmos Stones with a beam and, against everyone's pleads, merges them, forming the Dark Pterosaur. He makes it charge up Gigas, Armatus, Maximus, and Brontikens with extra power. Spectre tries 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 vs. MaxEdit
Chomp attacks Cryolophosaurus, but it dodges, so Chomp uses Ultimate Thunder. However, Cryolophosaurus sidesteps the final bolt of lighting and rushes, knocking Chomp back and cancelling his attack. Cryolophosaurus uses Snow Crystal, and Max recalls Chomp just before the attack hits.
Seth vs. D-TeamEdit
Rex summons Ace, Zoe summons Paris, and their DinoTector forms are activated. 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 newly-created Final Thunder Move Card, which he uses to defeat Cryolophosaurus.
Seth vs. D-Team/Alpha GangEdit
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 PiratesEdit
The Space Pirates teleport down with their dinos and launch a surprise attack.
Maximus uses Spectral Punisher to defeat Terry and Paris at once, Gigas uses Spectral Lancer to defeat Chomp, and Armatus uses Spectral Stinger to defeat Tank, Spiny, and Ace in sequence for a commanding victory.
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'?"
(Gel Jark teleports down from Backlander to Seth)
-Rex: "He's got the Cosmos Stones!"
(Backlander sways and nosedives)
-Ursula: "And I'm guessing he got Jonathan."
(Backlander crashes loudly atop the D-Lab's hill)
-Dr. Z: "Forget Jonathan—MY SHIP!"
-Seth: "The Stones are all mine. But don't fret, you get something too. But I doubt that you'll like it! Snow Crystal!"
(Spectre is levitating the Cosmos Stones from the wrecked D-Lab)
-Zoe: "The Cosmos Stones!"
-Spectre: "That was too easy. Finally, I have all seven of the Cosmos Stones! Ah-ha-ha-ha!"
-Max: "He's merges it, them!"
-Zoe: "Don't do it!"
-Rex: "It's too dangerous!"
(the Cosmos Stones merge and blink out, a shadowy miasma spreading in their place, taking shape…)
-Dr. Owen: "Whoa! What on earth is happening!"
-Max: "Wait a sec. Is that…the Pterosaur? But, something's wrong."
-Shear: "Way to go, boss."
-Foolscap: "The universe is yours. Uh, you plan on sharing?"
-Gabbro: "Yeah, can I have a moon somewhere?"
(Spectre is leading the Dark Pterosaur up to his ship)
-Max: "Oh no! Spectre, you're crazy! You don't know what you've done!"
-Rex: "But I have a feeling he's about to find out. The hard way."