Tempest 2000 modifies the gameplay of the original Tempest by adding power-ups, bonus levels, more sophisticated enemy types and wildly varying web level designs. The game features a total of 100 web levels, with new frame colors and variations after every 16 levels completed. In all versions, progress is automatically saved after completing a couple of levels and players are allowed to resume by using "Keys" to return to the last stage where the game was saved. There are also three gameplay modes in addition to the main game. Completing all 100 web levels in Tempest 2000 unlocks "Beastly Mode", which is a harder difficulty setting where enemies move faster, fire more often and are more resilient to the player's shots. In addition, the player's ship fires at a lower rate than in the original difficulty.
The main objective of the game is to survive and score points for as long as possible by clearing the playfield on the screen from enemies that appear at the bottom of the web. The player's ship has rapid-fire capacity to quickly shoot down enemies within the same segment the player is positioned at. The ship is also equipped with a Superzapper smart bomb that destroys all current enemies on the playfield, while recharging the Superzapper and using it a second time destroys a random enemy on-screen.