You do need to use the skyline. When you go through the first small tunnel look left as soon as you emerge from it and you will see a platform attached to the airship. Jump onto that.
There is a Patriot in there and some regular men you take out.
Destroy the engine then turn look left and jump out of that doorway back onto the skyline and then immediately down on to the dock you first jumped from to get onto the skyline.
As soon as you destroy the airship engine it begins to move off. If you don’t jump off quickly you automatically die then start back at the beginning of the dock, however the airship is gone and the double doors you needed to get through are now open.