When a dinosaur from the Great Valley wanders into Station Square only to disappear abruptly, the searchers follow its tracks. What they find in a large hole where it entered from is a shocking revelation: the Great Valley is being erased from history by Bowser's time-traveling forces, and that dinosaurs from that world have begun to get abducted and transported across time and space to random locations by the shenanigans caused in the seige. The very hole that our heroes entered into is a by-product of one such rip in the timestream continuum.
In fact, the very reason why the Great Valley is being destroyed is that one of the Chaos Emeralds just happens to be located there and it's needed by Dr. Blowhole to recharge the power cells of the Omega Doomship and the Technodrome. Of course, Littlefoot isn't going to stand by while his homeland is being torn to shreds by time-ripping Koopa Troopas, and so rallies up his friends to take back the Great Valley, heal the timestream to save his friends, and stop Blowhole from gaining the Chaos Emerald in the process.