The captain showed Sayid and Desmond images of the crash of Oceanic 815 at the bottom of the sea. Widmore's people believe (as far as we know) that Ben put the plane there. But last night, we see Ben's people (Tom, aka Mr. Friendly, who is later killed by Sawyer, or so we think) tell Michael that the crash was hoax planted by Widmore.
So who put the plane there? Tom had pictures of the graves from Thailand and the purchase of the plane, which is very convincing that Widmore put it there. But we also know Ben can make things magically appear just by thinking about them with his "magic box".
Ben had Alex go out to the temple so that he could get his daughter back with his people and safe from the oncoming war between the survivors and Widmore's people. He had his people wait until they arrived on the trail to the temple and ambushed them. Karl (the boyfriend) was killed so that Alex would be safe (this includes safe from getting pregnant). Rousseau was an unfortunate casualty of the cross-fire.
Sadly, Rousseau spent 16 years on the island staying alive by focusing on her own well-being. As soon as she stops caring about just herself and focusing on her daughter, she dies. The lesson? Care too much about other people and you're dead. Think about this logic, and it helps justify what Michael had to do (at least a tiny bit).
But how is Ben in touch with his people? And what good will $3 million to do Miles when he's held prisoner by Locke? Why only $3 million?
Cool tidbit from Lostpedia: Before his death, Karl says, "I've got a bad feeling about this." This is a line that is spoken in every episode of Star Wars.