While Helga and the Alpha Gang take down the Gel Jarks with salt, Rex and Zoe intercept Seth, and Max catches up. Suddenly, the Space Pirates' ship rams 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. The Pirates' ship collided because its engines went out when they first collided; the parents are making milkshakes, wishing their kids were there to enjoy them too. Seth nearly defeats Ace and Paris, but Chomp takes down Cryolophosaurus with Dr. Z's newly completed Move Card, Final Thunder; however, Seth and the card vanish. Rod and Laura gather six of the Cosmos Stones, but Seth has left with the Black Stone in an escape pod, leaving behind a retracted Gel Jark ball.
Spectre contacts the D-Team offering to trade the Cosmos Stones for their parents and they accept, but when their ships dock to make the trade, the parents refuse to let it happen, even as both the D-Team and Spectre try to convince them to. Dr. Cretacia throws a paper airplane to the kids and Dr. Ancient orders Jonathan to leave immediately; Jonathan must obey and leaves, and with broken engines, the Space Pirates can't follow. The D-Team realize the paper airplane is actually three pages: Max's mother's recipe for milkshakes, Zoe's mom's recipe for apple pie, and Dr. Cretacia's recipe for extra soft cookies; Helga comments she was created shortly after Dr. Z's only attempt at making a similar special recipe for brownies for the Alpha Trio as kids. Then Jonathan then concludes something shocking. Back at the D-Lab, Reese can't properly contact the Backlander, before her, Dr. Owen, and Patrick are startled by Cryolophosaurus and Seth.
Jonathan has traced Seth's escape pod as arriving in the present, following a communication signal from the D-Lab; Seth contacts them and tells them the only way to save their friends is to hand over the six 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 already being sucked into the time portal, crashing through the Pterosaur and entering the present. Upon arriving, they teleport down with all their dinosaurs in armor to confront Seth, who activates the Gel Jark ball 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 Seth's old lightning rod, teleports down with the other Cosmos Stones, letting the Backlander crash. Cryolophosaurus knocks down all their dinosaurs with Snow Crystal, Seth and the Gel Jark rushing into the D-Lab pursued by Dr. Z riding Helga. Just then, the Space Pirates arrive and attack, defeating all of the D-Team and Alpha Gang's dinosaurs, missiles from Armatus' Spectral Stinger also wrecking the D-Lab with Seth and Dr. Z inside.
Spectre floats down to lift out the 7 Cosmos Stones with a tractor beam and, against everyone's pleads, merges them, forming a dark cloud that shapes itself into the Dark Pterosaur; he makes it charge up Gigas, Armatus, Maximus, and Brontikens with extra power and a hazy aura. He leads it back to his ship, but as he tries having the ship absorb its energy, the cloud encompasses the ship, flooding over the Space Pirates, and the Dark Pterosaur increases monumentally in size! The end of the universe and all of space and time is nearing…
Seth/Cryolophosaurus vs. Max/Chomp
Chomp charges Cryolophosaurus, but it dodges, so Chomp uses Ultimate Thunder. However, Cryolophosaurus sidesteps the final bolt of lighting and rushes up, knocking Chomp back and cancelling his attack. Cryolophosaurus uses Snow Crystal, and Max recalls Chomp just before the attack hits.
No result (advantage Seth)
Seth/Cryolophosaurus vs. D-Team
Rex summons Ace, Zoe summons Paris, and their DinoTector forms are activated. Paris charges, but Cryolophosaurus knocks her away with its tail, only for Ace to trip it. Max re-enters the battle with Chomp already summoned and armored.
After a short interruption of the Space Pirates crashing into the Backlander, Cryolophosaurus uses Blizzard Smash, knocking Paris and Ace aside. Chomp attacks Cryolophosaurus, but it dodges, hits him, then dodges again. Dr. Z runs up and gives Max the newly-created Final Thunder Move Card, which Chomp uses to defeat Cryolophosaurus.
Seth/Cryolophosaurus vs. D-Team/Alpha Gang
Seth is waiting with Cryolophosaurus summoned and threatening Reese, Dr. Owen, and Patrick, while the D-Team and Alpha Gang teleport down from the Backlander with all six of their dinosaurs summoned and armored.
After Seth explains his true plan for the Cosmos Stones and downs the Backlander, Cryolophosaurus uses Snow Crystal at the group, streaking past the people and pelting their dinosaurs, knocking them across the battlefield. As Seth abandons the battle, the Spectral Space Pirates arrive.
No result (advantage Seth)
D-Team/Alpha Gang vs. Spectral Space Pirates
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, and to wreck the D-Lab.
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. How 'bout 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!"
(the Space Pirates call out their finishers)
-Shear: "Spectral Punisher!"
-Gabbro: "With the side of Spectral Lancer!"
-Foolscap: "And for desert, Spectral Stinger!"
(Spectre is levitating the Cosmos Stones from the wrecked D-Lab)
-Zoe: "The Cosmos Stones!"
-Spectre: "Ya-hahahahahahaha! That was too easy. Finally, I have all seven of the Cosmos Stones! Ah-ha-ha-ha!"
-Max: "He's merging, 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."
-Max: "Guys, remember what the Pterosaur said? About all of space and time being destroyed if the Cosmos Stones were merged? Well, I think is finally happening!"
- When Cryolophosaurus knocks Paris away and is then tripped by Ace, it is following a recycled animation sequence used by Gigas in The Wee Musketeers.
- As the Space Pirates' dinosaurs are powered up by the Dark Pterosaur, Saichania's arcade roar is heard despite each of their distinct roars also being heard.