The concept for this is relatively simple: Maps using this game mode are elongated with 3 intersecting paths leading from one end to other.
One team is the Defenders, and they are guarding a massive cargo ship (or something else appropriate to the setting, as I don't really know or care about the Lore of GoI). They start at one end of the map, with the Transport with them at a random spawn leading into one of the three paths.
At each intersecting point the Transport may choose to change to a different path at random, so it's impossible to predict where it will be at any given point. Transport Ship is relatively durable, and has an auto-repair for the armor that functions like a crew trying to keep the ship intact. The armor only repairs when not taking damage for whatever amount of time is balanced.
The Defenders always know where the Transport is (both on the map, on the compass, and as a Marked target with a distinct color to differenciate it from the Enemy Targets). When killed, Defenders can respawn at any intersecting point along the map, but only those closest to the Transport are active.
Attackers have to destroy the Transport. They do not have any way of knowing where it is, and spawn at the far end of the map to begin. If at least one of their ships has sight of the Transport, Attackers can spawn at points two spawn points away from the Transport. If the Defenders guard the Transport all the way to the opposite end of the map from where it started, they win. If the Attackers destroy it, they win.
The Transport moves slowly. It may take a full minute for it to reach a new Intersection from the previous one, and a map could have between 5 and 10 Intersections along it, depending on the map. Another variable is to increase the number of paths from 3 to 4 or more. When one team wins, the teams switch from Attackers to Defenders and vice versa. If the event of a tie, a tie-breaker occurs with the teams swapping one more time, and the Transport spawning only 2 Intersections away from the end.
EDIT: To clarify something before it comes up, a Squid could probably go from one end of a path to the other in about a minute, maybe a minute and a half, depending on the size of the map. This is of course adjustable on a map-by-map basis, but that should give a general idea of how slow I picture the Transport itself moving in comparison to the speeds the other ships can achieve. At the longest, I could see it taking maybe 2 minutes for a Squid to reach from one end to the other.
And before someone asks why there are random paths, it's because otherwise this is just mobile Capture the Point of a sort. With this random element to it, scouting is necessary, as is having enough firepower to take on the enemy's four ships, then later defend the Transport when it's your turn. This encourages more diverse ship combinations than 4 Pyras or 4 Galleons or something, as that just won't work with both Attackers and Defenders.