The game opens with Bomberman flying in a spaceship back to his home planet accompanied by a strange egg, when his ship is sucked into a black hole. Bomberman loses consciousness, and later awakes to find himself in a jail cell with the mysterious egg, but without the Fire Stone that allows him to use his trademark bombs. The egg hatches shortly afterwards, and the creature that emerges introduces himself as Pommy. Pommy is able to slip through the bars of the cell to retrieve Bomberman's Fire Stone, and with it Bomberman is able to escape. The two later learn that they were imprisoned by henchmen working for the Astral Knights, an evil group collecting the seven Elemental Stones. Bomberman and his new friend set out to stop the Astral Knights from executing whatever they're planning.
The Story Mode has eight levels, each one a planet with a different theme. Each planet has a boss fight against one of the Astral Knights, six of whom carry an elemental stone. Gameplay is much like that of Bomberman 64, although 64's spherical explosions have been replaced with the traditional cross shaped explosions found in 2D entries of the series. One of the biggest additions to The Second Attack are the new types of bombs that Bomberman can use. After most boss fights Bomberman collects a new Elemental Stone that allows him to use a new type of bomb. These new bombs often must be used to advance past certain sections, such as using ice bombs to freeze water or wind bombs to blow Bomberman across a gap.
The other big addition to The Second Attack is Pommy. At first Pommy can aid Bomberman by stunning enemies, but he can evolve into stronger forms with different attacks if Bomberman collects enough food. The type of food that Bomberman collects will affect what Pommy evolves into. Pommy can either be controlled by the AI or a second player.
The Second Attack features five multiplayer modes; Survival, Battle Royal, King & Knights, Key Trial, and Score Attack. The options allow players to change the number of rounds it takes to win and the amount of time in each round. Some modes also have options for ghosts, sudden death, and shuffle.
Survival Mode is the traditional Bomberman multiplayer mode. Four players try to blow each other up, and the last player left standing is declared the winner.
In Battle Royal players receive ten points for killing another player, and lose five points for dying. The player with the most points when time runs out wins.
In King & Knights the players are split into two teams and must protect an inanimate king while trying to kill the other team's kings. Each king has either 4, 7, or 10 hit points depending on how the player set the game up. Players can pick up and move either king, which is an integral part of ensuring they're safe.
In Key Trial two keys are hidden within objects in the map, and players compete to collect both keys. If a player with a key is caught in an explosion they'll drop it, allowing any player to pick it back up. Unlike most other game modes, Key Trial is played in split-screen.
In Score Attack players compete to accumulate the most points before time runs out is the winner. Points are acquired by blowing up animals or containers, and collecting the food they leave behind. Like Key Trial, Score Attack is played in split-screen.