The Depot is the port to the rest of the world. This is where money, loot, and hostages are delivered, to then be taken into the base. There are two Depots on each of the islands, one Dock Depot and one Helipad Depot. When something arrives at one of the Depots, a minion will go and take it to the base.
The Helipad and dock are separated by a considerable walking distance, especially on Island 2 which is much larger. Therefore many players build 2 entrances to their base (each entrance close to one of the depots) in order to make the deliveries smoother and speed up the AoIs. This has an obvious disadvantage of giving agents easier access to the base. In the end, both possibilities can be used, depending on which option the player finds the most practical.
One interesting fact about the depot is that once agents reach its "sphere of influence" they are effectively on safe territory. Thus an agent marked with a kill tag, being shot at by minions as he/she runs towards either the helipad or the dock, will be safe as soon as they reach it. Minions will, infuriatingly, stand around for a while when the character "disappears" from their sight, while the target walks calmly into the depot, and with it, safety.
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