Littlefoot notices a Longneck herd entering the Great Valley and informs his grandparents, who tell him that the Longnecks are their cousins and that they must go and greet them. Upon the herd's arrival, the Old One, the herd's leader, tells the Great Valley's residents that her herd has been migratory ever since a heavy period of rain turned their old home into a marshland called "The Land of Mists" and became the home of many dangerous creatures. Later, Littlefoot meets a female Longneck named Ali and invites her to play. He introduces her to his friends, but as she is not used to associating with diverse species, she is afraid of them.
Meanwhile, Grandpa falls severely ill. The Old One notes that the illness is lethal and that no dinosaurs recover from it unless they eat the petals of the "Night Flower", a flower which can only be found in the Land of Mists. Though Littlefoot is warned that the Land of Mists is too dangerous, he becomes determined to save his grandfather and asks Ali to take him there. She agrees on the condition that Cera, Ducky, Petrie, and Spike don't come, claiming that they will slow them down. As the two of them make their way, they pass through a cave and a sudden earthshake causes various stalagmites and stalactites to come crashing down, separating them. Ali decides to return to the Valley and convince the others to help her free Littlefoot. Meanwhile, Littlefoot tries to find a way out and meets an old Archelon named Archie, who offers to help him dig through the rocks.
As they work, Littlefoot and Archie are interrupted by a Ichthyornis named Ichy and a mostly-blind Deinosuchus named Dil, who intend to eat them. Ichy and Dil pursue Littlefoot and Archie, but are knocked out when Ali and Littlefoot's friends dig a hole in the rock wall and send rocks tumbling down on them. Archie shows them a way to the Land of Mists and reminds them to stay close together before departing. In the Land of Mists, Cera is separated from the group. The others meet a mouse that Ducky names Tickles after his fur, which tickles her when she hugs him. Immediately after, Tickles helps them find Cera. However, Cera falls into a river and is pursued by Ichy and Dil, who have now recovered from their prior knockout. Ali saves Cera and distracts the predators, after which Cera softens towards Ali. Later, Ali explains her prejudicial behavior, having never interacted with species outside of her own, but remarks that her attitude towards Littlefoot's friends has now changed.
When the seven stop for the night, they realize they are in a field of Night Flowers after they bloom, and quickly stock up on them. As they make their way home, Ichy and Dil return for another attack. During the chase, Petrie is grabbed by Ichy, who intends to eat him since his small size leaves him barely enough meat for him. However, Tickles acts fast and saves Petrie by moving Dil's tail into the path of Ichy's sharp beak, tricking him into biting it rather than Petrie's stomach. Dil starts to attack Ichy over this, giving Petrie the chance to escape and rejoin his friends, but the chase resumes when the predators hear Cera laugh at them from a distance. The chase climaxes when Ducky, while retrieving a Night Flower, is nabbed by Ichy, fought over by him and Petrie, who tries to rescue her, and winds up falling into a river after the fight results in a draw. The fall into the river temporarily knocks her unconscious. Dil unknowingly fishes her out of the water, and when Ichy alerts her that she has, she then attempts to eat her, flinging her into the air with her snout and intending to catch her in her jaws when she comes back down. Spike then speaks for the first time by calling out Ducky's name, which awakens her in midair and prompts her to grab a tree branch to save herself. Dil then makes a few attempts to snatch her by jumping up at the branch, but she completely mistakes Ichy for Ducky when Spike knocks him down toward her open jaws with his tail after he mockingly vows that Littlefoot and the other children are his and Dil's next targets. As Petrie rescues Ducky from the predators, Ichy and Dil get into an argument over Dil trying to eat Ichy by accident. When they dismiss each other, Dil flings Ichy off with her tail. But then, she is pursued by a hungry plesiosaur called a Hydrotherosaurus (who rescues the kids from Dil) after calling desperately for her partner.
With the predators defeated, the children say goodbye to Tickles and head home. They give Grandpa the blossoms, and he gets better a few hours later upon eating them. Ali then leaves with her herd, but not before trying to convince Spike to say goodbye, which he does not, as he is too interested in consuming leaves. The narrator concludes that Littlefoot and the others would indeed meet Ali again one day.Scott McAfee as Littlefoot
Candace Hutson as Cera
Heather Hogan as Ducky
Jeff Bennett as Petrie / Ichy
Rob Paulsen as Spike
Juliana Hansen as Ali
Tress MacNeille as Ali's Mother / Dil
Linda Gary as Grandma Longneck
Kenneth Mars as Grandpa Longneck
Charles Durning as Archie
Carol Bruce as Old One
Frank Welker as Tickles
John Ingle as Narrator
The songs are written by Leslie Bricusse.Grandma's Lullaby - Grandma Longneck (Linda Gary)
Who Needs You? - Ichy and Dil (Jeff Bennett and Tress MacNeille)
It Takes All Sorts - Ali, Littlefoot, Cera, Petrie and Ducky (Juliana Hansen, Scott McAfee, Candace Hutson, Jeff Bennett, and Heather Hogan)
An instrumental version of the song "If We Hold on Together" appears on the soundtrack.
The film was released on December 10, 1996, on VHS and April 1, 2003, on DVD.
Joe Leydon of Variety recommended it to young children who enjoy Barney & Friends. TV Guide rated it 2/5 stars and wrote, "Memories of Don Bluth's engaging original The Land Before Time continue to grow dimmer with this indifferent sequel to the animated dinosaur saga." Michael Sauter of Entertainment Weekly rated a letter grade of "B" and wrote, "But if the formula hasn’t changed, it hasn’t fossilized, either." In August 2014, the New York Post ranked each of the 13 Land Before Time films released up to that point and placed Journey Through the Mists at number 7. The New York Post praised the character of Ali for adding "a little more girl power" to the series.