Hack//Outbreak is the third of a series of four games, titled . hack//Infection, . hack//Mutation, . hack//Outbreak, and . hack//Quarantine, features a "game within a game"; a fictional massively multiplayer online role-playing game (MMORPG) called The World which does not require the player to connect to the Internet. Players may transfer their characters and data between games in the series. Each game comes with an extra DVD containing an episode of . hack//Liminality, the accompanying original video animation series which details fictional events that occur concurrently with the games. The games are part of a multimedia franchise called Project . hack which explores the mysterious origins of The World. Set after the events of the anime series . hack//Sign, the games focus on a player named Kite and his quest to discover why some users have become comatose as a result of playing The World. The search evolves into a deeper investigation of The World and its effects on the stability of the Internet.

After draining the third Phase, Kite and BlackRose are shocked to find the Lambda server corrupted. Kite encounters Mia, who isn't acting like her normal self. Mia lacks her usual energy and is not in the mood to join Kite. At Mac Anu, Mistral reveals that she is a pregnant housewife and as a result can't continue to aid Kite despite her wish to see the adventure through to the end. As a result of these events happening at around the same time, Kite begins to doubt if he is doing the right thing, much to the dismay of BlackRose. Even so, Kite continues to follow clues wherever he finds them. At Σ Chatting Snaring Twins, Kite travels the dungeon alone and picks up data left by Harald. At the bottom is Balmung fighting a Data Bug by himself. After Kite helps him defeat the anomaly, the two talk and finally decide to join forces, agreeing that they need each other's power. Balmung leads Kite deeper and into another white room, this one with hundreds of butterflies in it.