The name of the video game references Lagrangian points, the five positions in space where a body of negligible mass could be placed which would then maintain its position relative to two existing massive bodies.

Lagrange Point has the distinction of being the only game ever released with Konami's VRC7 sound generator Integrated Circuit, which allowed for a drastic improvement in the quality of the music and sound effects used in the game. However, it drastically increased the price of the game to around 8500 yen. The game was never localized for a North American or European market. There is a current, although stalled, translation effort undertaken by Aeon Genesis.

In the 22nd century, mankind has begun to emigrate into outer space. Constructed at a lagrange point were three huge space colonies: the Isis Cluster (two artificial biospheres, named Land-1 and Land-2, and a satellite). In the year Isis 0024 (55 years after the cluster was constructed), however, a biohazard outbreak occurred on Land-2. All attempts at contact were met with nothing but static. Now a research team led by pilot Jean approaches Land-1.