Following the Border Worlds conflict of Wing Commander IV, the galaxy is once more at peace. Colonel Christopher Blair, hero of the Confederation has transferred into the Naval Forces. Blair helps design the TCS Midway, a state-of-the-art multi-role carrier that will help keep order during the Confederation's new peacetime. The luxury of peace allows Confed to retire many older pilots and assign younger pilots to piloting roles. Lance Casey and his friend Max "Maestro" Garrett are two such pilots, fresh from the academy, transferred aboard the TCS Midway along with several others for its maiden voyage along the borders of Confed Space. But soon into the mission, the Midway intercepts a distress call from the Kilrathi, the remains of a race of cat-like warriors who lost the war with the Confederation...Wing Commander: Prophecy is a space combat simulator. Players take the role of Lance Casey on his new assignment aboard the ship. The player can click various hotspots aboard the ship to engage in non-interactive FMV conversations with shipboard personnel. By entering the briefing room, players can receive full instructions on their next mission.Space Combat begins by launching from the TCS Midway carrier, and are displayed as first-person perspective inside the cockpit, similar to the rest of the Wing Commander series. Mission objectives vary between escort duties, patrol missions, search and destroy or defense of the TCS Midway herself. Depending on the ship being flown for the particular mission, the player will be able to switch between guns, missiles, torpedoes and mines with which to combat the enemy. The player, as wing commander, can give orders to nearby wingmen and communicate with any other ship. After each mission, the player must return to dock with the TCS Midway and will receive a mission performance rating.