As far as I can tell, the dark room used to be the maintenance entrance to some sort of underground highway/subway, as we can tell from the EP1 room and the subway room, I do not know when it could've been closed down, possibly due to some zombie infection, but we do know that the recent combine invasion was recent, as they are still pulling troops into the dark room. The portal near the start could be from the start of the invasion as the base for an invasion into the depths of the dark room. The lab likely had nothing to do with the actual dark room, as there is no connection to the lab and the portal hallway besides the park, which could be from temporal disruption from the portal, which could explain why there is no door connecting the hallway and the lab and the pit, both of which are in close proximity to portals.

The first portal was definitely used for transporting important objects, it is possible these also allowed for spreading the zombie infection, explaining the zombies and crabs in the supply room. Scavengers have also found the dark room, explaining the rebels, you could even be a scavenger yourself, it was also likely that the company or government maintaining these hallways rented out certain rooms to companies and individuals which would explain the office and Kleiners lab. Terrorists also carried out operations in the area, it could also be that they used it as an escape route, this could possibly be another reason why it was shutdown.