An updated version of the game was released in 1999 that made numerous changes to the original version. This is perhaps most notable in the story, which while still sharing the same premise and plot outline, removed or changed various plot points:

• The original version had a subplot where LapTrap received what the game referred to as "wisdom of the village elders", in which he experienced visions of the villagers' pasts, providing possible motives for why they would want to steal the treasure. This was also how the ClueFinders obtained their clues, which appeared as beams of blue light that zapped LapTrap and gave him the info. The entire subplot was removed in the revision, with the original cutscenes being replaced with new ones featuring the ClueFinders discussing theories about the disappearances instead. Likewise, clues were obtained in a more typical fashion of talking to NPCs and having them share information with you.
• The fate of the true culprit behind the thefts, Spoiler:the apprentice, is different in both versions following his burial under an avalanche. In the original version, he escapes from the snow only to be dragged back under by the real Yeti. In the revision, however, this was changed to him simply climbing out and declaring that the ClueFinders can't stop him.

In addition, the series' art style was updated in 1999, leading to the graphics, and character sprites and content from the animated cutscenes being updated in the revision to better match it. Several music tracks were also added to areas that were silent in the original version.