The number of action points is determined by the character's attributes. Both sides take turns to move and perform actions, which uses their action points. When player characters and enemies are in the same sector, the game switches to turn-based play. The player is limited to a single save slot during the day. The player may move the mercenaries to one adjacent sector. The player can now directly command his chosen mercenaries and issue movement orders. When the player has chosen the mercenaries and equipment to take to the mission, he is taken to the sector he chose earlier overseeing his mercenaries from a top-down viewpoint. These requests can be ignored but usually cause some kind of hindrance to the player at a later date. Occasionally, Jack or Brenda Richards contact the player with an important objective, such as securing a clean water source.

Mercenaries can be left at the base to either heal, train skills or repair items. Mercenaries, guards and tappers need to be paid if needed, the player can raise the guards' and tappers' salaries to make them happier. The player can also decide what mercenaries and equipment to take and what player-owned sector to start from. The map includes information such as the number of Fallow trees in each sector, whether the sector is enemy or player controlled, how many guards and tappers are in a sector and the terrain information.

When the player starts a new day, the game is transferred to a screen displaying Metavira on a square grid. Here the player can load and save the game, change settings, hire new mercenaries or sleep until the next day. The player starts the game and every following day in a room. ) to reclaim the island from Santino's forces sector by sector. There, Brenda and her father request that the player hires mercenaries through the Association of International Mercenaries (A.I.M. When the game begins, the player is contacted by Jack Richards and is invited to the island. He immediately began to recruit new people and gradually took over the island by force.

Santino consequently established a new base on the other side of the island. He managed to convince Jack Richards, the leader of the scientific mission, that it would be beneficial to have two independent science teams. Her assistant, Lucas Santino, realised how profitable this sap would be. However, Brenda also discovered that the trees could not reproduce. The nuclear tests altered some trees on the island and several years later it was discovered by a scientist, Brenda Richards, that those trees, known as Fallow trees, produce unique sap that proves to be a medical marvel. Jagged Alliance takes place on the fictional South Atlantic island of Metavira, a former nuclear testing site.

Jagged alliance 3 cancelled