Here’s my take on what’s going on:
Flight 815 crashes on the island. Ben is now worried that there will be a huge search effort underway which will eventually uncover the secret of the island. So, he fakes the crash to end the search and make everyone go away.
Desmond blows up the hatch, which exposes the island. Whidmore discovers this, and sends a freighter there to see what’s up. They discover the wreckage of 815, and recover the black box. This is the evidence they need to show that the other crash was faked, and to bring down Ben and his organization.
Remember, they are at cross purposes - Dharma and Whidmore want to exploit the island - open it up for health tourism, use it to make wonderful devices, whatever. Ben wants the island to himself. He wants it hidden.
So now Whidmore has the black box, which he can take back to civilization and show everyone that the crash was staged, and put the kibosh on Ben’s operation. But the freighter is stuck because Ben’s man sabotaged it. So Ben temporarily has the upper hand.
Now, my guess for what’s coming is that Michael will sabotage the black box and erase it, getting rid of Whidmore’s proof. So how to prove the crash was faked? Hey, take back the 815 survivors. That’ll blow the conspiracy wide open.
Now, here’s another problem - how does Sayid wind up working for Ben? So far, Ben’s looking pretty evil, and the Freighter guys pretty good. So here’s a wild guess - it’ll turn out that Ben iis the good guy after all - not personally decent (he’s not), but his cause will be right. Why? Because the island is too dangerous. If it becomes public, it’ll wreak havoc on the world. Time travel, magnetic anomolies, you name it. So Sayid will come to realize that it’s critical that the existence of the island remain secret, so he joins forces with Ben (who has his own reasons for keeping it secret), and starts whacking all of Whidmore’s people.
There are some holes in this - wouldn’t the island already be common knowledge, because the Oceanic six are celebrities? I don’t know. Maybe there’s a big coverup involving the six of them and they have a different story to tell. Maybe a condition of their rescue with is that they could never mention being on an island, and the rest of the losties are essentially hostages to keep them from talking. Maybe Whidmore’s decided to keep it to himself, and he’s trying to get rid of Ben and keep the secret so he can exploit it.
And if the other losties are hostages, then the ‘Oceanic Six’ would have had an incentive to tell the authorities that they were the only ones left (Whidmore would kill them if they revealed it). That opens the door to the possibility that Jin is still alive - Sun had to get off the island for the safety of the baby, but Jin might have been kept behind as a hostage to keep her from talking.
That might also explain why Hurley said “Good” when Sun said that no one else was coming. Maybe there are people watching them, and having all the losties get together like that would draw too much attention.