The Portal is a unit that allows for quicker ship and ammunition travel between multiple places. Packets and ships will find the closest portals going from their current location to their destination, and will go through them to shorten their travel.
For ship travel, at least two portals are required. For ammunition packets, a minimum of one portal is required, and the Apex Ship will send ammunition through the nearest portal (think of it as the Apex having its own built-in portal).