Players: 1 - 2
Difficulty Options: Easy, Normal, Hard

The Marathon Mode is an endless mode which has you set a difficulty (Easy, Normal, Hard) as well as a speed for the blocks to rise up. Here, you select your Pokémon and you go into a stage to get as high a score as possible. As you progress and get higher scores and combos, the Speed of the game will increase

In multiplayer mode, the combos you make will cause garbage blocks to fall on the opponent and the match ends when either player loses.

Players: 1
Difficulty Options: Easy, Normal, Hard, Super Hard, Intense

Challenge Mode is one of the main features of Pokémon Puzzle Challenge. This mode mirrors the story of Pokémon Gold & Silver and has you play as Gold as he goes through the Johto region playing against Gym Leaders.

This mode is a simple bit of play where both you and the Gym Leader are playing. When you get combos or chains of over 4, you will do attacks that damage the opponent while if they do it, they will fill your puzzle area with blocks that need to have a combo touch them in order to turn into standard blocks, much like the other modes.

If you manage to achieve certain combos, then other characters will appear in the path and will challenge you, offering you their Pokémon if you beat them. In addition to that, if you lose a match, you lose the use of that Pokémon for the rest of your campaign.

This mode can be played in Easy, Normal, Hard, Super Hard or Intense difficulties, with the characters appearing different based on your difficulty.

Players: 1 - 2
Difficulty Options: Easy, Normal, Hard

Time Zone is a lot like Marathon Mode but rather than playing until you get a game over, your task here is to get the most points you can within the 2 minute counter. When the time is up, your score will be given and added to your records.

Players: 1 - 2
Difficulty Options: Easy, Normal, Hard

Line Clear mode is a unique mode in that it has multiple saves for you to access. This gives you multiple levels based on each of the Gym Leaders of the Johto region and has you have to clear all of the blocks above a certain line. Once you have done that, you will pass the stage and go to the next. There are 5 stages for each Gym to complete.

Players: 1
Difficulty Options: None

Puzzle Mode is a mode where you are given multiple puzzles to complete. These puzzles are combinations of various blocks that you need to completely clear. There are over 60 puzzles to complete. You can reverse any move you made with the B Button or get a hint from Professor Oak using the Select button. You get 3 hints for each Round.

Once you have completed 8 stages, you can proceed to the next round.

Players: 1
Difficulty Options: Easy, Normal, Hard

Garbage Mode is a mode akin to Marathon Mode, but as you play, you'll get lots of garbage blocks falling from the top that also need to be cleared. The game continues until you have hit the top of the screen.

Unlike Marathon Mode where your Speed increases depending upon how well you do, this time the size and frequency of the garbage blocks increase.