January 22, 2012. The D-Team, along with Max's dad, paleontologist Spike Taylor, went to a dig site somewhere in Japan, to investigate a possible dinosaur tooth found. However, further analysis suggests that the "dinosaur tooth" was just a tusk from a pig. Unsatisfied, the team decide to walk back home, until Max notices a sign advertising a resort town called Ninja Village. Although reluctant at first, Rex and Zoe manage to convince Dr. Taylor to go with them.
At the resort, Dr. Taylor and Max are enchanted by the sheer realistic-ness of the costumes, until a manager, dressed in a ninja attire approaches them and invites the D-Team to an attraction where owners and their pets try to croos a ninja obstacle course. However, without a dinosaur or any other pet, Max has to be left aside.
At the end of the obstacle course, only Rex and Zoe are left, and because Dicky burrowed through the wall of the rock climbing wall (the last obstacle), Rex and George won. The manager (still dressed in a ninja costume) hands Rex a scroll with pictures rouchly translating to "I Love Dinosaur King".
Meanwhile, Dr. Taylor is watching a live performance of two ninjas fighting. However, on of them turns on a fan, which carves at a rock wall behind the stage, revealing the articulated fossil remains of three Deinonychuses, the Center Stone, and a tablet bearing three separate carvings. When the other warrior raises his sword, refracted sunlight bounces off it, onto the fossils, making a pack of ferocious, rainbow-colored, glowing Deinonychus appear!
At Upsilon Dot, Z, M.D is watching the Deinonychus on the news, and not knowing of the Secret powers of the dinosaurs, think that the rainbow aura they emit are signs that Z, M.D. (or Doctor Z for short) are going to catch them. Not wanting to lose a chance, Dr. Z and the Beta Pack fly to Ninja Village on a nuclear-powered plane. However, instead of brakes, the B-Team are ejected onto square parachutes, which tangle up and turn into a fan-like shape, slowing down the plane (which still crashes).
Later, both the D-Team and the B-Team separately go into a ninja funhouse filled with trapdoors and hidden passages, all just barely missing each other. Later, as each separately find their way out, they are greted by Dr. Z, and he's about to confront the Deinonychus!
Trying to save Dr. Z, Mursula summons Sister. She uses Volcano Burst, but then, the three Deinonychus bite each others' tails, and swing them at Sister. Max is surprised! According to Compy, it was a Super Move called Whip Attack. Before Sister has a chance to attack again, the three Deinonychus perform another equally deadly attack: the Spinning Attack, which did great damage on Sister! Then Deeno orders Dano and Sue to run fast through Sister. They've just performed Crossing Attack!
Then its the D-Team's turn to attack. First, Zoe calls out Dicky, whom the Deinonychus are already scared of. She then uses Thorn Whip to corral the Deinonychus trio to a single area. Then, Rex has George perform Fire Cannon on the huddling Deinonychus Trio, who are defeated. Max then claims their card, and calls the three individuals, Deeno, the leader of the pack with a feathery crest, Dano, a male member who has lots of dark spots, and Sue, a female member with considerably few dark spots.