The series tells the story of Ginji Amano and Ban Mido, a pair of superpowered individuals known as the "GetBackers". The duo operates a freelance repossession service out of one of the seedier areas of Shinjuku, Tokyo. For a fee, they will recover any lost or stolen item for a client with "a 100% success rate". The GetBackers' job often leads them into bizarre and dangerous situations in order to "get back what shouldn't be gone". Their targets range from lost video games to misplaced components of an atomic bomb. The plot mostly revolves around their adventures, often complicated by the pair's convoluted, individual pasts and a mysterious place known as the Infinity Fortress.
A conglomeration of disused, condemned buildings clustered together to form a self-contained habitat, Limitless Fortress is subdivided into three specific tiers – Lower Town, the Beltline and Babylon City. Lower Town is the lowest in altitude, with several layers extending below ground level. The Beltline, the most dangerous area of The Limitless Fortress, is ruled by Der Kaiser, Ban's father. Babylon City, the upper most level of the Limitless Fortress, is said to be where the Brain Trust resides, and is the home of Ginji's mother. In actuality, Babylon City is what one might consider the real world, with everything else being a virtual reality creation. Only those who have won the Ogre Battle may enter Babylon City and when that happens, they can change the world as they see fit. Both Ban and Ginji go to the Fortress with Ban wishing to rescue a kidnapped Himiko from Kagami, and Ginji finding a possibility to meet his mother. Going to the Belt Line, the GetBackers encounter various warriors taking orders from a being known as Voodoo King from Babylon City. The Voodoo King seeks to obtain three "keys" which will help him unlock the gates from Babylon City sealed by Ban's grandmother several years ago. After finding the three keys: Shido's chimera spirit, Himiko's mirror and the GetBackers, the Voodoo King is faced by Ginji whose Lightning Lord alter-ego attacks him in a clash which destroys both beings. Following this, both Ban and Ginji face each other in Ogre Battle with Ban giving up, impressed with Ginji's will. Ginji goes to Babylon City where he meets his mother from a parallel universe, who explains how she created the Fortress and its surrounding world. Following a discussion between the two of them, the Fortress' world remains unchanged except that the virtual people living become real beings. Ban and Ginji continue their retrieval job, ending the series when requested to go on a mission that will lead them to meet Ban's mother.
The plot of the anime adaptation of GetBackers follows the manga's closely until the first season's ending. The second season features various stand alone episodes focused in the GetBackers' missions, while also two story arcs, the second ending the anime series with an open ending.