After the climax, in which the pirates discover that the map did not lead them to the treasure and subsequently mutiny against the baffled Long John Silver, Treasure Island ends with the treasure recovered. After Dr. Livesey and his party fire on the pirates, who scatter in all directions, it is revealed that Ben Gunn had dug up the treasure some time ago. After finding it, he moved it to his cave.

Jim and the non-pirate members of the crew take the treasure with them on the ship. They are able to load it onto the Hispaniola over a period of three days while Jim packs the coins into bread bags. They leave the remaining three pirates on the deserted island, but Long John Silver comes with them, despite no one trusting him. During their voyage back to Bristol, Long John Silver manages to steal some of the treasure and sneak overboard with it (Jim presumes he returned home to his wife, briefly mentioned earlier in the novel).

Once the Hispaniola returns to its original destination, everyone divides up the treasure for their share. Captain Smollett retires in comfort, and Ben spends all of his share quickly before becoming a lodge keeper. Jim does not say much of himself, save that he is haunted by dreams of the pirates and that he never plans on going back to the sea, let alone treasure hunting.

What happens at the end of Treasure Island and what could be an alternate ending?

The Long John Silver character was such a great one that I hated to see him disappear entirely at the end. I would like to have seen Long John return in some manner--be it in America or back on English soil. A satisfactory scenario for me would be including a prologue, several decades in the future, where an elderly but still scoundrelous Long John reconciles with the adult Jim Hawkins. Perhaps Silver has another treasure map to share with Jim, and maybe Jim would be trusting enough to follow him on one more adventure.

What happens at the end of Treasure Island and what could be an alternate ending?

At the end of the story, the captain and the other "good guys" leave all the mutineers who are still alive behind on the island.  All, that is, except for Long John Silver, who comes with the good guys.  They sail the Hispaniola to some unnamed city where Silver escapes.  The other five return to England and share all the wealth that they got.

As far as alternate endings, it could really be anything that catches your fancy.  The story actually has a happy ending, right?  All the people that you like end up rich and happy and the bad guys get what they deserve.  If you don't like an ending like that, make another one up.

You could say, for example, that the Royal Navy boards the Hispaniola and thinks that all of the men are pirates because they have pirate treasure.  Or you could say that Silver (maybe with Gunn's help) kills the other four and takes all the treasure -- not just one bag.  Or you could have one or more of the "good guys" turn bad and kill the others and take the treasure.  There are all sorts of ways to end the story...