Identiical Twins living in the Post-Apocalyptic Caribbean have their village attacked by pirates, one of them is taken and the village is destroyed; unable to make contact one devotes his life to saving his brother while the other slowly becomes identical to the very pirates that pillaged his town.

>>After all that search, we discover that the niece has grown to be closer to her kidnapper who raised her than her biological family.

Not only that, the John Wayne character, Ethan Edwards, initially wants to kill her for that reason. (Another possible plot point : what would the good brother do upon discovering that the leader of pirates who have pillaged and plundered his community is his brother?)

I love that idea.
The movie "The Searchers" with John Wayne has a similar theme. After all that search, we discover that the niece has grown to be closer to her kidnapper who raised her than her biological family.

Another possibility would have both brothers making very different choices for the same reason.
Two identical brothers, same background, same education, two completely different choices lead to two completely different lives. Something bad happening to their shared love interest (injury, rape, ...) could be the reason. While being apart, they are still close together as both brothers still compete for the love and affection of that woman. Both trying to support her using their own personal situation. The pirate by smuggling drugs and weapons. The villager by bringing food. Until the big showdown.

There is a French book about that same situation during the Second World War between two brothers. One is resistant, the other is a collaborate ur. When one killed, the other one decide to assume both identity. In order to restore their brotherhood and avenge his brother, he erase (kills) all the person involved in their lives. Their shared love interest is the only one who at the end realise what is going on, but We the reader never find out which one was killed.

>>He?s going to know, but it?s not going to stop him from doing what he has to do to survive.

My concern with this it that in the 3rd act, it seems to be a weak choice for a leading character -- even if he's the bad guy. (The pirate is the villain, isn't he?)

A character might act to merely survive in the 1st Act, but during the course of the 2nd Act, he should grow through his character arc (for better or worse) to be able to act for some purpose other than merely to save his skin.

So that at the climax in the 3rd Act, he willingly risks all -- including his life -- for some cause, some purpose, or (strongest and best of all choices) to save the life of someone else (a stakes character or stake community).

Oh i definitely intend to. When I put up the logline I really just wanted to get the idea out there so it was a very rough draft. I think dpg?s version is on point and with a tweak or two it?d be perfect

Interesting for sure. I tend to agree more with "dpg" interpretation of your logline. You have a great story to tell but the logline needs to be shortened by taken unnecessary wording out. I would tweek dpg's suggestion and make it my own.

Trust me there are some very important details in the story that root in the setting, just sort of think lostish with towns. This post-apocalyptic caribbean is where everyone went if they escaped. They're worn down but not absolutely horrible. Also pirates were not very common before the setting of the story, they were sometimes thought of as myths bc they never had came to the islands. They are from another continent or chain of islands and are on a mission to harvest anything they can from every island they see.

He's going to know, but it's not going to stop him from doing what he has to do to survive. The other brother will not know it's his own brother bc of his pirate pseudonym until possibly the very end he might talk to him on the radio as he basically waits to die. I want the destruction to be an h-bomb from far away so they never meet face to face

The base idea is interesting if your story is about "...how two identical people in different circumstances can become completely different.".
However I think you may be adding unnecessary complications to the story with the setting as there is no inherent need for the apocalyptic archipelago location.

More so this specific type of post Apocalypse doesn't conjure up in my mind an image as clear as other post Apocalypse settings such as; Mad Max 2 - out back Australia, THX1138 - underground urban USA, Snow piercer - future ice age, etc...
Closest I can think of to this is; Water World which, location aside, simply didn't work as a movie.

Okay, but if they are separated as teens, how credible would it be that the pirate brother is acting unwittingly, in complete ignorance? That he doesn't remember, ergo doesn't recognize, anything about the area, or anyone?

That's what we were saying except have them start out as like 13-14 and end around the early 30's. Also I want the pirate one in the end destroy his home town and brother unknowingly.

Thirty years after infant twins become separated by pirates, they unwittlingly face off in a war for survival, one as the leader of his tribe, the other as the leader of the pirates.

Half the show is the life on the island after the attack where they are gearing up to fight back against future attacks, while the other half is the one brothers rise to pirate infamy. It basically shows how two identical people in different circumstances can become completely different.