Warning, this could be considered spoiling.
The guys on the boat miraculously float back to the island. The guys that took Walt? Part of the Island, and Walt was taken to punish Michael for leaving the island. They want Walt for his developing skills as a psychic, and possibly the ability to manifest his thoughts into real things. (Or the things he thinks of are manifested against him to scare him into not using his abilities.)
The hatch? Access port to a weapons testing facility, and emergency escape. The island was used for old Naval weapons test, and due to treaties, had to move everything underground. The ’security guard’ is there to prevent people from gaining access to the underground bunker. The trees blowing out of the ground? Left over blast power from weapons testing harnessed to scare the crap outta people.
More random survivors will appear, the survivors of the tail section. They will cover a few more back stories, but not do all 40-whatever, since no one will know how to keep track of that many.
The plane was shot down by the US military to prevent it reporting the location of the island, under the plausible grounds of national security. Besides, what survivors would there be to tell what they saw if anything.
In the end, just about everyone dies. (Eventually.) Locke finds out he’s just a madman with a really good imagination when he finally learns the truth, and kills himself. Jack dies to save Kate. Kate dies of execution in a prison somewhere in the US. Hurley, after surviving running around on a tropical island without so much as a minor hear attack finally keels over when he finds his mother has squandered the 156 million, and he’s once again a pauper going to work at a fried chicken place. Michael dies trying to win the affection of his son, and Walt lives on to be a psychic in the US until an enraged client kills him for not telling him the whole truth. Everyone else on the island dies when the Chinese nuke it to prevent weapon development after the story is leaked. Except for Saeed and Vincent, who survive the blast, and make it back to the US. Saeed is put in an Arab internment camp after another terrorist attack, and is killed trying to save a young American boy. He becomes a martyr, and the American fascist regime crumbles to the ground.
Vincent finds Brian, the wanker who gave up Walt because ‘he’s kinda creepy’ and bites his nads off, then pees on his face. He goes on to be the new lassie in movies, and lives a long, healthy, scientifically extended life paid for by Hollywood. (The new capital of the US.)
Oh, but before all that happens, hopefully HBO will buy the show and show it like it would really be - people giving up on social conventions, and really going naked when they naturally would. (So far the only nudity on this show has been the Korean chick, and it was just to create a moment of awkward bonding. Please. In that situation, lots of those people would be screwing like bunnies, cause there isn’t much else to do.)
Hey, don’t say I didn’t warn ya.