Sawyer makes a deal with Charles Widmore, something is locked in the sub

Sawyer makes his way into the submarine where there is another armed guard. Zoe leads him down a corridor past another guard who is seems to be guarding a room with multiple padlocks on it. Sawyer aks about it, but Zoe tells him it's none of his business.

Sawyer enters the office and Charles Widmore introduces himself and extends his hand, which Sawyer does not shake. When Sawyer says that he knows that Widmore sent the freighter to the island to kill them all. Widmore replies "It's sad, really... how little you actually know." Widmore then tells Sawyer that his team did not kill the Ajira passengers either, but he doesn't expect Sawyer to believe him.

Sawyer tells Widmore that he'll go back to the main island and tell Locke that there was no one on the island as long as the people on his own boat are not harmed and are given safe passage of the island. Widmore agrees to the deal, but seems very skeptical that he can trust Sawyer.

So what is Widmore keeping in the locked room? Is it a person or a thing? Also, what is Widmore's mission on the island? Since his people are setting up the sonic fence, it seems that he wants to keep the smoke monster away, but whose side is he really on?