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The gameplay is nearly identical to the first The Treasures of Montezuma
game. Players must align three or more gems of the same color to clear them off of a board, all the while destroying specific gems that contain crystals within a time limit in order to progress to the next level. Several power-ups are also included, specifically color based "totems" that activate various abilities when two consecutive sets of a specific colored gem are cleared. These effects range from adding more time to painting all of the gems a different color.
The majority of the game is similar to the original, though a few new additions are in place. Power-ups and upgrades are now done by building small temples on a "town" map, and several new power-ups are now available. The level selection process is much more streamlined, and no longer includes an overworld "map," but rather a linear display of all levels across all three difficulties (one higher than the previous installment). The previous game's star-tapping bonus game has been replaced, now with a scavenger-hunt type mission at the end of each set of levels that requires the player to find various pieces to prehistoric treasures for bonus points.
New gems are also included, including a "frozen" gem that must be destroyed twice. The achievement system of the original game has been expanded, now with more achievements and actual point values for them. A new Endless mode has also been added to coincide with the game's Puzzle mode.