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Let's say you find a mod that will put a really excellent camoflage pattern on your hull. If you can't find what you want, ask your favorite mod maker. In short, anything your heart desires may be available someday. Instead of "All ahead Flank" think of Montgomery Scott saying "Captain, the engines can't take anymore!" Smoke stacks with My Little Pony or the Chicago Cubs icons on them. Imagine a clock you can read without squinting. The color and size of the text and on the GUI. For instance showing ship weapon ranges in their icons. The details and content of the player lists on the side of the screens. The details of your aircraft, and who wouldn't want a scout plane that looks like a navy blimp or mono-planes instead of bi-planes. The details of your weapon sprites, basket ball shaped shells flying through the air, and sharks instead of torpedoes. The details of your ship, anything from narhwal shaped bowsprits, to mermaid figureheads, to enormous "Eat At Joe's" signs on the hull. The cursor reticle and grid marks in binocular view, numbered for easy reference and colored like a rainbow. So mods may be available that will change almost any thing you can see or hear in the game. While it is sad that no one else will see my St Louis that looks very much like the tragically lost USS Maine, with the proud, breton sporting, black sheep standing on the prow (kidding), we work with what we have. To the other players your flag will be the standard flag that comes with the game, or whatever flag their mods have flying. But you will be the only one to see the brave double headed eagle. So if you don't like the flag that waves on the back of your ship and want to replace it with the Battle Standard of the Duchy of Grand Fenwick you may find a mod that will do that for you. But it only effects the interface on the computer that it is installed on. It can change aspects of what you see and in some cases what you hear when you play.
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A mod is a "Modification" to the user interface of a game. Instead I shall try to explain what a mod is and how you can apply and use them. There are no mods that will do that for you, and there are too many mods to discuss in one thread. If you opened this thread hoping to find out which mod will make you the supreme frag god of the universe, I fear I shall disapoint you.
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