This article contains spoilers about a hidden element in CP3D. It is suggested that if you have not found this yourself then you do so before reading this article.
The Engine Room was presumably constructed by Rory as indicated by the notes in the Pipeline and it is where the islands water is processed.
An Unwelcoming Flood
Some time before the mini-mission, A Welcoming Flood that took place during the Water Party 2020, the Water Engine was damaged. This cause the islands water reservoir to increase in pressure which lead to the underground pool 's windows to crack. This mini-mission seems the player navigating the Pipelines of the island to reach this room in order to repair the damage.