On the Space Pirates' ship, Dr. Ancient realizes that the Cosmos Stones have been merged. On the ground, as the Alpha Trio searches through the wreckage of the D-Lab, Helga erupts from the roof, carrying Dr. Z, and the Gel Jark drags out Seth, but they run from the charged-up Gigas when he appears behind them. The Space Pirate dinosaurs shoot off their charged Spectral Moves across the city, causing extensive damage, as the Dark Pterosaur looms overhead, disheartening the D-Team.
In the forest nearby, Helga shorts out, and the Alpha Trio begin to praise Dr. Z's memory until he wakes up. Then, while remembering everyone who will be lost if the give up now, including Chomp, Max has a realization, and gives a motivating speech to get everyone willing to keep fighting on. He says that their best chance is the Stone Plates because his Dino Bracer had repelled the Black Cosmos Stone earlier. Reese then adds how Seth said that the Stone Plates were positive and the Cosmos Stones negative, so they should equal and cancel each other, Dr. Z saying to merge the Plates to match the merged Cosmos Stones. When Rex comments they can't combine the Stones and attack with their dinosaurs at once, Seth says he can make more copies of the Stones.
On the Backlander, after Reese repairs Jonathan, Dr. Z and Seth come out with the Copied Stones. However, Seth tells them that once their dinosaurs are summoned into their full-sized forms with the copied Stones, they can't be put in their pet-sized forms again. The D-Team and Alpha Gang accept this and give themselves a few more minutes to enjoy their dinos as small pets, before calling them back, setting the Stones in the Backlander's panel, and flying up to the Dark Pterosaur, whose shadow streams become purple lighting in response.
Within striking distance on top of the Backlander, they summon and armor their dinosaurs and attack: Chomp with Lightning Strike, Ace with Sonic Blast, Paris with Emerald Garden, Terry with Magma Blaster, Spiny with Hydro Cutter, and Tank with Spike Arrows. The six blasts form a Fusion Move that hits its target, but only rips a hole in the Dark Pterosaur's outer shield, so they fly inside to finish the job. However, as soon as they enter, floating images of Spectre and the rest of the Space Pirates appear and challenge them with Gigas, Armatus, and Maximus, and then Brontikens, but the Pterosaur protects them from attacks, and though the Alpha Gang's dinosaurs fall (taking Gigas with them), the D-Team eventually wins. After spotting the Space Pirates' ship (and detecting dinosaurs aboard to convince Dr. Z), they dock and the D-Team runs to find Max's house, but their parents aren't there. Meanwhile, Dr. Z finds Spectre's dinosaur cages, getting a message from the parents that they're in the bridge. After finding them, the D-Team finally reunite with their parents, but Jonathan takes the ship's controls, as Seth has taken the Backlander!
As Seth pilots the ship, the spectral images of the Space Pirates try to stop him, but he flies through them. Having seen how he was blinded by the Cosmos Stones' power, he has resolved to destroy them to keep them out of anyone's hands and, with the Pterosaur wrapping around the Backlander, smashes into the actual Dark Pterosaur in the heart of the larger outer shell. The Stone Plates glow and vanish into energy beams shooting out through the Dark Pterosaur, in a cosmos-folding explosion clearing the sky of the Dark Pterosaur and presumably destroying both the Stone Plates and Cosmos Stones. A message from the Gel Jark on the Backlander now floating on the ocean tells Jonathan that Seth is injured but still alive.
In a Mesozoic bio-dome projection on the surface of the Backlander, Dr. Z celebrates his rescue of the dinosaurs from the Space Pirates' ship, and how they all love him for it, letting him finally become the Dinosaur King! Nearby, the Alpha Trio, D-Team, Rod and Laura, and Dr. Owen and Patrick ride on dinosaurs amid a large group, Dr. Owen of course chasing Ursula. Meanwhile, Dr. Ancient and Dr. Taylor discuss that the dinosaurs' live essence was in the Stone Plates, having formed after their spirits merged following being wiped out by the arrival of the Cosmos Stones (despite Seth's earlier explanation, but both are likely just theories). Helga, the mothers, and some Alpha Droids have also cooked lunch.
Later that evening, after fixing the D-Lab and the city with the Space Pirates' ship's restoration wave, Rex and his family are ready to leave, but Dr. Z is unwilling (until Helga convinces him). They will be unable to return again, as the Backlander's engines are completely destroyed, and the Space Pirates' ship's engines can only make one more time jump. Dr. Owen makes one last rejected marriage proposal to Ursula, Zander giving a flag-filled flower to Reese. Rex says he will start a branch of the D-Team in the future, but when the Alpha Trio tries to join, Zoe slips in one last "old lady" comment to Ursula. Dr. Drake also gives Dr. Z his gigantic needle.
Everyone from the present is teleported down to the D-Lab, Max and Zoe saying their last goodbyes as the Pirates' timeship leaves, vowing to always remember their friends.
Elsewhere, Spectre and the Space Pirates float through space in a pod, with Foolscap and Shear complaining about Spectre's singing, and when Gabbro offers to sing along, they reply with a big "NOOOO!"
D-Team/Alpha Gang vs. Spectral Space Pirates
Ed and Zander are out
Maximus and Armatus use Spectral Punisher and Spectral Stinger again, but the Pterosaur appears around the Backlander and blocks them with an energy shield. Chomp then uses Lightning Strike, Ace uses Sonic Blast, and Paris uses Emerald Garden, the three attacks hitting at once and defeating Maximus and Armatus.
Shear and Foolscap are out
Gabbro and Ursula are both out
Power-charged Brontikens is summoned from nowhere by Spectre and uses Spectral Destroy, but the Pterosaur keeps protecting the Backlander. Chomp uses Ultimate Thunder, Ace uses Ultimate Wind, and Paris uses Ultimate Leaf, the attacks hitting together and defeating Brontikens. His card flies down at them.
(the Backlander is flying into the Dark Pterosaur, but hears deep humming)
(giant looming image of Spectre appears in front of them)
-Spectre: "What are you little tykes doing here?"
(images of the other Space Pirates also appear)
-Shear: "They always seem to find some way of showing up and being a pain."
-Max: "That's right, and if you thought that was painful, just wait. Now call all this off or you'll be sorry!"
-Spectre: "Having the ultimate power in the universe means never having to be sorry. Not for chewing with your mouth full, not for being five minutes late to the opera…not for destroying the entire planet Earth! Ah-ha-haha!"
-Foolscap: "Don't worry, he's not going to destroy Earth."
-Gabbro: "At least not before we have some fun with you first."
(the Space Pirates' dinosaurs are summoned into existence)
(the D-Team's sad goodbyes, for real this time)
-Max & Zoe: "Bye!"
-Max: "Take care, Rex."
-Zoe: "We maybe times apart, but we'll always be friends."
-Rex: "Yeah. For all of time."
(present-time people teleported to the surface)
(Rex looks at his D-Team badge, his parents put their hands on his shoulders)
-Dr. Cretacia: "We'll all miss them, Rex."
-Dr. Ancient: "Time to take off."
-Jonathan: "Right. Off we go."
(commandeered Space Pirate Ship flies off)
-Max & Zoe: "Goodbye! See ya later!"
-Zoe: "Bye, Paris, I'll never forget you."
-Max: "Take care, Chomp. Goodbye, Ace."
(ship leaves through time portal)
-Max & Zoe: "You guys will always be in our hearts."
(meanwhile, floating in a pod through deep space…)
-Spectre: "Ooooh~, space is fine~, space is divine~…"
-Foolscap: "How much longer do we have to listen to you?"
-Shear: "Well, seeing how space is infinite, I'd say forever."
-Gabbro: "Would it help if I sang along?"
-Foolscap & Shear: "NOOOO!"
- The animation of the Fusion Move forming to approach the Dark Pterosaur is recycled from the Black T-Rex battle, having several rainbow beams from Secret Moves instead of any yellow beams for a Lightning Move, which were absent from that battle, though the main rainbow beam resembles yellow close enough for the quick shot seen in this episode.
- When the Space Pirates' projections taunt the Backlander, an animation error occurs with Gabbro's mouth: the mouth properly on his face doesn't move, while a second copy of his mouth's layer, the one that actually speaks, is placed down over his chin.
- At the end of the episode an Isisaurus can be seen among the free dinosaurs of the Space Pirates, and even if never officially confirmed, it can be assumed that it is Genie.
- With the exception of Genie, the Deinonychus trio, Anhanguera, Tupuxuara, and an Ophthalmosaurus, none of the dinosaur species used by the Space Pirates against the D-Team/Alpha Gang can be seen at the end of the episode. This makes it more likely that almost all of these dinosaurs were instead from Dr. Ancient's expedition (contrary to the dub's dialogue), supported by the specific species present being known members of the D-Team/Alpha Gang's Move Card dinosaur collection and some examples of unique behaviors:
- The Saurolophus pair were probably the same from Dinosaur Amour!, being a couple.
- The Daspletosaurus was probably the same from Dance Evolution, as seen in his style of dancing.
- The Iguanodon obeying Dr. Owen to follow Ursula was probably Iguano from Ruff and Ready, who had befriended her.
- The Deltadromeus was probably the same from Battle Royale, as can be seen from his preference to swim butterfly-style though the ocean.
- Others, like Supersaurus, Seismosaurus, the Pteranodon, Velociraptor, and Deinonychus trios, Fukuisaurus, Pawpawsaurus, and Futabasaurus, are likely from season 1 as well, despite having no noticeable quirks to be identified by, while the Tupuxuara, Anhanguera, and Ophthalmosaurus were likely from the Move Cards retrieved from the Pirates during season 2.
- How a Microraptor was present on the Backlander is unclear, having never been associated with a Dinosaur or Move Card to be possessed by a character in either season, nor, if wild, having seemingly had a chance to stow away on the Backlander during its Jurassic trip. It was possibly included in error for the purposes of having a wide selection.