edit: i now realize that guild flagships have been suggested before, but this suggestion sees them as more of a big co-op warship than a base, a common theme in other flagship suggestions. If you all want, I could just change it to flagships being team based rather than guild based.
thank you @anon38832104 for pointing this out
Flagships for teams, storyline, dungeons, etc.
Details/background
enemy npc portion
These would be large ships that could potentially appear in the Dark Sea as stationary dungeons, because moving ships is a pain when most attacks freeze you in place, but they could just have a mechanic where they just stop moving after you take out everyone on the top deck.
The ships would have several decks, as well as the generic crew quarters, brig, etc.
These ships wouldn’t have anything too special, just your run-of-the-mill dark sea loot. maybe there could be loot themed around insanity or something, due to months or even years of exposure to the dark sea. Another idea would be special tattered sails or worn figureheads or lanterns.
The flag and faction of the ship could be any kingdom or organization in the game, as there’s probably at least a few people in each kingdom who are crazy enough to be in the dark sea.
There could possibly be a friendly npc version of this encounter, which could offer an exclusive crew type or co-captain.
wait, this is just pirate encounters but on a bigger scale
throw in a chance for a lost spell or primordial or something. These crews have been in the dark sea for a while, and may have found a scroll or two. Obviously, the droprates would still be low.
team/co-op kind
You could also purchase these sorts of ships, or do a chain of side quests to get one.
These ships could function as a spawn for you or the team you are in, unless near important storyline locations, bosses, or the dark sea, in which case the spawn will default to each member’s storyline progress.
The warship would also have an above-average amount of ship slots available, to encourage people to work together to efficiently manage the ship.
there could potentially be different types of warship, specializing in things such as speed, defense, and weaponry. Steam-power is also implied to exist in the war seas, so an upgrade could be offered to convert the warship from sails to steam-power, decreasing the effect of wind at the cost of speed.
The ship owner, team leader, and elite members would be able to add figureheads, ship weapons, and sails. They would also be able to change the layout of the ship itself. However, only the ship owner would be able to change the color scheme of the ship.
oh, and these ships would still be able to have crew, but maybe the ship could have several crew types
Reason to add/change
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lets be honest, it’s more fun traveling the dark sea in a single boat rather than a fleet
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Bigger encounters would be interesting
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Ships on a larger scale would help promote cooperation between players
Q: isn’t this a bit far-fetched?
A: yes 
Q: Why teams and not guilds?
A: if you wanted to go on an expedition into the dark sea or something, everyone would have to be part of the same guild. This way, people can work together without having to be in a guild.
