- Flash Columns, where the playfield is pre-filled with five rows of jewels and players must clear specific flashing tiles to clear the stage. Based on the mode of the same name from the original game's home release, this version includes multiple goal tiles (which are no longer necessarily at the bottom of the playfield) and Skulls (dangerous tiles that, when cleared, raise the bottom of the playfield). At every three levels, there is a bonus stage where players have a limited amount of time to "throw" tiles upwards at a large group of jewels to clear them. Like the original game, a second player can join-in for simultaneous single-player play.
- VS. Columns, in which two players compete to outlast each-other in normal Columns play. Players can raise their opponent's playfield (and simultaneously lower theirs) by clearing a larger line of jewels at once (one row for each line of four, two rows for each line larger than four) and performing combos (one row each). A special version of the Magic Jewel column is used with three special tiles to cycle through (the bottom-most tile determining the effect): one to clear all jewels of the same type it lands on, one to raise their opponent's playfield, and one to lower their playfield. Only a limited amount of rounds can be played with each credit, and the game does not switch to the single-player game for the winner.
In addition, the game switches between four "themes" each Flash stage or VS. round, changing the background art, jewel pieces, and music. Keeping with the "The Voyage Through Time" theme, this includes a pre-history theme (with fossils) to a sci-fi futuristic theme (with simple shapes). It is also notable for supporting sit-down "cocktail cabinet" configurations with players at each side of the machine.
An enhanced version of the game (made by M2) was digitally released for the Nintendo Switch in Japan on August 8, 2019 as part of the Sega Ages series, with an overseas release on October 17, 2019. This version includes new game modes and online multiplayer, as well as an enhanced port of the original Columns.