Before actually playing the game, there are two boards to select from: the Ruby field and the Sapphire field. While both layouts are quite similar, there are enough differences to separate the boards apart.
The game follows standard pinball rules. A small ball (in this case, a Poké Ball) moves around the board, striking different objects in order to accomplish certain goals. When it falls towards bottom of the board, the set of flippers must be used to force the ball back up the table. If the ball escapes the flippers and reaches the bottom of the board, that ball is lost. When all of the available balls are lost, the game is over. There are two main goals to this game. The first is to earn points, which are acquired by performing a variety of actions. The second goal is to complete the Pokédex. Whenever a new Pokémon is acquired, it is added to the Pokédex.
The game starts from a "standard mode" until a special mode is activated. The special modes are: Catch 'Em Mode, Egg Mode, Evolution Mode, and Travel Mode. There are also bonus levels that are accessible.
Catch 'Em Mode
Catch 'Em Mode is where a Pokémon can be caught. To activate it, send the ball through the Right Loop two or three times (Sending the ball through the loop three times allows for a rarer Pokémon to be available for capture). Then send the ball into the Sharpedo (on Ruby Field) or the Wailmer (on Sapphire Field) to start the mode.
After Catch 'Em Mode is activated, the Pokémon Panel shows the silhouette of the Pokémon available to be captured and the clock starts at two minutes. Send the ball up to the bumpers. If the ball hits any of the bumpers three times, the Pokémon will appear out of the panel. Hit it three times to capture it. If the clock runs out (or the ball is lost), the mode is over and the Pokémon is not caught.
Should a catch be successful, one Poké Ball out of three will light up under the silhouette window.
Egg mode is where a Pokémon hatches from an egg. It is activated by hitting Cyndaquil four times (on the Ruby Field) or by hitting it through the Egg Loop four time (which is between the Right Loop and the Wailmer on the Sapphire Field). The Pokémon will hatch from the egg and there is a set (but hidden) time limit.
The Pokémon will crawl across the bottom of the board. Hit it with the ball two times before it goes back to the cave (on the Ruby Field) or the shop (on the Sapphire Field). If the catch is successful, another Poké Ball lights up under the silhouette window.
Evolution Mode (or Evo Mode) is where a Pokémon that was previously captured can be evolved into another Pokémon. Unlike in the original Pokémon Pinball, Evolution Mode is only available when there is a Pokémon that is capable of evolving.
To start Evo Mode, send the ball through the Left Loop three times. Then hit the ball into the Poké Mart (the Mart does not have to be opened by any other way). Choose the Pokémon that you would like to evolve to start the mode.
The Pokémon that is trying to evolve appears and the clock is set at two minutes. A small evolution item will appear somewhere around the board. Hit it with the ball and repeat two more times. Then the Center Hole will open. Hit the ball into the hole to complete the evolution. If you lose the ball or the time runs out, the evolution fails.
When an evolution is successful, the player gets not one, but two more Poké Balls lighted under the silhouette window. As there are three balls under the window, there will be no carrying over of lighted Poké Balls should two balls have already been lit up and another two are added.
When the game begins, one of seven areas is selected. Each area is home to a unique set of Pokémon that can be captured in Catch 'Em Mode. Travel Mode allows for that area to change. To activate Travel Mode on the Ruby Field, hit the Chikorita Switch and then hit the Linoone on the left side, and repeat two more times. To activate Travel Mode on the Sapphire Field, hit the Seedot Switch (which is next to a basket) on the left side of the board, and repeat two more times. When activated, the timer is turned on for one minute.
Send the ball through either the Left Loop or the Right Loop and then hit it into the Center Hole. Then you are given the option of whether you want to travel or not. If you travel, the area is changed.
If you Travel 6 times, you will go to the Ruins. Pokémon up for Capture are Regirock, Regice, Registeel, Beldum, and Jirachi (through Roulette), no matter if you use two or three Capture Arrows.
If three Poké Balls are lighted up under the silhouette window, the player gets to play in a bonus stage (one may decline if they wish to). There are five different bonus stages, similar to the original Pokémon Pinball series, two each exclusive for a table and a fifth that is accessible from both tables, but only after certain conditions have been fulfilled.
Unlike in the original game, whatever stage the Ball is in when it enters the Bonus Stage stays with it, allowing a higher bonus. However, the stage of the Ball will degrade one level if the player loses it.