Plot
In the Late Cretaceous period, a young Tarbosaurus named Junior is chased by a Tsintaosaurus. His enraged father, Speckles, shows up to rescue him as killing a Tsintaosaurus. An enraged Speckles scolds at Junior as he could have been killed and for not fighting back (and also due to the fact that Junior is all Speckles has left).
Speckles takes Junior up top a hill and teaches him a lesson on how Speckles' ecosystem is his kingdom and agrees to make tomorrow his first hunt.
The next day, Speckles says that Junior is the same species like him and to just go over fears. However, when Speckles is hunting some Protoceratopses, Junior's fears come back to him, and was thrown and ends up in the water. He can't swim (As Junior has become aquaphobic from being washed out to sea in the first film), so he calls for help, despite being in shallow water. An enraged Speckles is disappointed in his son's cowardice. However, he over-reacts and lambasts Junior for his inability to conquer his fear. Hurt by his enraged father's comments, Junior tells his enraged father that he hates him and the pair storm off from one another.
Later that night, Jr. has flashbacks about the death of his mother. Speckles comes to him and tells him that this world is full of dangers, yet is also full of wonders.
The next day, Jr. is hunting a Pachycephalosaurus, when five Deinonychus abduct him. Speckles pursues the Deinonychus, but two of them manage to knock him into a river at the bottom of a gorge, followed by a rainstorm that masks their trail, delaying the pursuit, but die in the battle. Junior later finds himself in a desert compound where many other young dinosaurs have also been kidnapped. A young Therizinosaurus named Slash bullies Junior, but a young female Tarbosaurus named Blue defends him. A Carnotaurus named Blade tells Slash to stop the fight. The Deinonychus return, gather all the other dinosaurs up and take three other dinosaurs away from the dome and out of sight.
Meanwhile, Speckles is still looking for Jr. He meets a Saichania named Cy, who wants to avenge the loss of his best friend Daisy at the claws of the same Deinonychus. Jr., meanwhile, befriends Blue and meets a Monoclonius, called Dusty, while looking for shelter. While passing through a deep, dark ravine, Speckles and Cy are attacked by five giant scorpions. Speckles is able to kill or injure all of them, but one of the scorpions manages to sting him on the leg, poisoning him. Afterwards, they escape the ravine.
Meanwhile, at the dome, Jr., Blue and Dusty are attracted by food. Dusty tries to eat some plants, but a Dsungaripterus named Dsunga steals them. Heartbroken, she lies in her cave, but Jr. and Blue bring her some plants and berries and she becomes friends with Jr. Elsewhere, meanwhile, Cy and a dying Speckles are on their way, when Speckles begins to hallucinate on seeing Junior, but it really isn't. That's when a sand dune starts to shake and they end up in a dark pit. There, they meet a female Tarbosaurus named Fang who heals Speckle's wound with herbs. After a short misunderstanding, Fang is revealed to be Blue's mother and is searching for her. She joins Speckles and Cy on their quest for the compound.
While Jr., Blue, and Dusty are playing, Ditto, one of the members of the pack, catches them and takes Dusty all the way up the dome. In return for food, the Dsungaripterus reveals that the Deinoychus are giving the young dinosaurs as sacrifices to a mysterious beast that lives in the local volcano. The beast in turn gives the young dinosaurs to his offspring as "toys" to play with, and when they get bored, they kill and eat them, which horrifies Junior, who blames himself for not stopping the Deinonychus from taking Dusty away.
Speckles, Fang and Cy meet a Pukyongosaurus herd whose eggs are being stolen by a marauding pack of Carnotaurus in an oasis. Speckles is initially reluctant as he's determined to rescue his son, so much so, that he tries to stop Fang from intervening the raid, callously demanding that "It's none of our business" much to Fang's dismay and the Tarbosaurs get into an argument. Fang chastises Speckles for his selfishness and reminds him that when he was poisoned she could've left him to his fate since it was his problem, not hers. But since Fang lacked Speckles's ruthless demeanor she decided against it. Fang then tells Speckles that if he can be on his way as she intends to help the sauropods before continuing on. Before Speckles and Cy could leave however, Speckles catches one of the eggs and decides to assist Fang with Cy following and telling Speckles that he can be a jerk sometimes. The bandit leader pleads for mercy, to which Speckles wisely grants, and the thieves retreat. The eggs begin to hatch. Fang states to Speckles that he did a good deed before he decides they must leave. When asked by Cy about the noise the sauropods are making, Fang explains it is how they communicate.
Back at the compound, Junior tells Blade to try and escape this area, so later that night, Junior distracts the Deinonychus, while Blade and Blue throw stones at them. But when they get to the exit, the 3 Deinonychus and Slash (who was revealed to have spoiled the plan to the raptors to sparing his life for the beast of Fire Mountain) are there, waiting for them. Immediately Junior, Blue and Blade try to escape, but were stopped to a dead end and were thrown back into their cave prison. Elsewhere, Cy, Speckles, and Fang are stargazing and talking about missing their loved ones.
The Deinonychus capture the Dsungaripterus, who are threatening to kill him, then, they chase Cy and have him cornered on a cliff. Speckles and Fang arrive and ambush them. Ditto is caught and interrogated by Speckles and Fang after being left behind and knocked off by Cy, and is eventually crushed by a brief earthquake. The pathway is blocked by boulders, but the same herd of Pukyongosaurus that the trio encountered help clear the rocks.
The volcano begins to erupt and the Dsungaripterus reports to the other dinosaurs there is a fight occurring. Meanwhile, Speckles, Fang and Cy fight the Deinonychus pack. Blade told the other dinosaurs to stampede out of the dome, because the volcano is erupting. Speckles, Fang and Cy search for Junior and Blue. Blade fights Slash and a pair of Deinonychus over a pit of lava, then, with Blue and Jr.'s help, sends Slash and the Deinonychus falling to their doom in the lava pit.
Speckles and Fang finally find Jr, Blue and Blade, who are running towards a river. Although Junior can't swim, he jumps in along with Blue and Blade. When they dive down, they find the cave the Dsungaripterus was talking about. There, they find Dusty being chased by three large iguanas. Luckily, Speckles and Fang are able to save them. However, an enraged Speckles once again, shows his strict attitude about Junior not being brave enough to take on the beasts without retreating. Speckles soon realizes the error of his ways after being scolded by Blue for taking Junior for granted. However, they are soon confronted by the beast, which turns out to be a giant iguana many times larger than a Tarbosaurus (And even a T-rex), and a fierce battle breaks out. After he and his friends lead the beast away from the adults, Junior sacrifices himself by letting the iguana hit him, which knocks him out, the iguana dies crushing by the rocks. Everyone mourns for an unconscious Junior who wakes up, making everyone relieved. Speckles apologizes to his son for being so hard on him and that he is happy that Junior is his son. The volcano starts to erupt, and the gang is able to escape after Speckles lures the same beast into crashing into the boulders.
Having finally arrived at paradise, Cy says goodbye to Speckles, Fang, Blue, Jr., Blade and Dusty, who all begin a new life together.
