On the H.S. Cale, after you've spoken with Admiral Sir Thomas and joined the coalition, you may encounter a certain NPC behind Sir Thomas, this NPC will be named Major Danny. When you start the conversation, he will give you the option to start the quest: Supply Line.

Major Danny tells you a ship with the crates landed at Cork, this is where you can find the first crate. The crate in question will be inside a red shipping container in the middle of the row to the left as you enter the shipping yard.

You may have searched the shipping yard top to bottom like me, and been clueless as to where the second crate is. It turns out, the second crate is North of Cork. Just follow the railroad track north until you reach Lad's Brewery, the crate will be under the crane in the North-West corner of the area.

Now, you could continue following the railroad tracks as they loop West and ultimately North however, it is much quicker to just drive offroad North-West to Arklow, which is where the third crate is. When you get to Arklow, walk to the West side of town, to the train station. This third and final crate will be on the platform, to the right of the main building.

Hurray! You've finished the quest, but now you have to turn it in. Return to the H.S. Cale, talk to Major Danny again, and turn in the quest.