These facilities are the primary means of transport between various levels and are often the target of level objectives in order to facilitate various tasks performed across multiple areas. After the Yard level, these are the sole spawn point for the Armor unit.

Trunk Ports are the primary means of what connects the various areas of the Darwin Simulated Life Research Project together. Data is transferred from one area to another, through these ports, and with it various integral parts of the Darwinian’s society. In the game the main purpose they serve to the player is to allow access to the next level, or to unlock a new spawn point in a level that has multiple trunk port connections.

There are various levels such as the Mine, where these facilities much be captured through the reprogramming of a nearby Control Tower in order to facilitate the transfer of materials from one area to the next, or in this case, raw polygons to be processed into the Armor units.

After completing the Yard level, the Trunk Port will begin to serve as the spawn point for Armor units in any level, this being because it must be transferred through the Trunk Port system from the Yard itself. It also turns out, that a misused Trunk Port has a lot to do with the virus disaster that has struck the Darwinians (see the temple level).