It first appears in the level "Under Attack" where it is freed by the Indominus rex smashing into the aviary. In the opening cutscene, three Dimorphodon that escape attack JW001, causing it to crash. They and Pteranodon then attack Main Street and its visitors. In the level itself, it is encountered in the first half as an enemy NPC.
Its last appearance in the game's story is in the level "Main Street Showdown" where 3 are seen perched on several rooftops watching the fight between the Indominus rex and the Velociraptors Charlie and Echo. Shooting all three with the plush toy launcher built in the level earns the player(s) a minikit. One more that is perched is encountered in the final half near a pile of dung on a high top to the left and soon flies away when one of the characters approach it.
The amber that unlocks Dimorphodon is found in the first level it appears in: "Under Attack". The minikits that can be collected from this level also unlock its skeleton and its skeleton skin as well. As a playable dinosaur in the game, it is much like the Pteranodon except it can not pull switches like the latter.
Despite being an enemy, Dimorphodon would never attack a human for food. It simply ate fish and insects as it was very small.