Mega Bomberman plays out over six different stages as the player sets out to piece Bomberman's world back together after it was struck by a mysterious comet. Each stage is broken down into levels, Bomberman must collect a tablet in each level in order to piece back a picture in the stage screen. At the end of each stage the final tablet is collected by fighting a boss. Each of the six stages have a theme they are respectively a Jungle, Volcano, Sea, Haunted House, Arctic, and Asteroid themed levels; this diversifies the grid that Bomberman plays on as well as the enemies it encounters.
Battle mode allows up to 5 players on the TurboGrafx-16 and 4 players on the Sega Genesis, and also allows computer controlled opponents. Each player is assigned a different color and may choose between 9 different Bomberman characters to play as, and teams can be determined. In total there are 10 different battle arena's to choose from, each having its own conditions that change the gameplay.
In addition to Mega Bomberman and Bomberman '94 is the use of a kangaroo type animal called Rooi. There are different colored Rooi's in the game and are found, at random, in Eggs as a powerup; each colored Rooi has a unique ability.
- Green Rooi - Allows you to dash.
- Purple Rooi - Allows you to jump over bombs and soft blocks.
- Blue Rooi - Allows you to kick bombs away from you, as well as over soft blocks.
- Yellow Rooi - Allows you to kick soft blocks.
- Purple Rooi - Can only dance, and has no special move that assists Bomberman.
Items are found by destroying soft blocks in each level. They appear at random, the most common items are the Bomb Up and Fire Up items, the rest appear only some of the time or are rare.
- Egg - Collecting an egg item will allow Bomberman to ride a Rooi.
- Bomb Up - Increases the amount of bombs you can set.
- Fire Up - Increases the range of a bomb's explosion.
- Speed Up - Increases Bomberman's walking speed.
- Speed Down - Decreases Bomberman's walking speed.
- Remote Control - Allows Bomberman to remotely detonate bombs.
- Wall Pass - Allows Bomberman to pass through soft blocks.
- Bomb Pass - Allows Bomberman to pass through set bombs.
- Bomb Kick - Allows Bomberman to kick bombs.
- Line Bomb - Sets as many bombs in a line at once.
- Recovery - Shields Bomberman from a single hit.
- Clock - Enemies are frozen for approximately 10 seconds.
- Fire Resistant Suit - Protects Bomberman from bomb blasts and enemies for approximately 20 seconds.
- One-up - Adds an extra life.
- Skull - Infects Bomberman with a virus, used only in Battle Mode.