Ben manipulates people to accomplish his personal goals. Most recently we see that he plays up the importance of the submarine so that Locke will feel that much more committed to his plans to blow it up. But in the end, we see that Ben wanted the submarine destroyed and just used Locke to further his desire.
In the recent Paulo & Nikki episode, we see that Ben and Juliette visited the Pearl to spy on the Losties in the Swan before Ben is caught by Danielle. We now know that his primary goal in this field trip was to coax Jack into wanting to remove the tumor from his spine.
But what about the bits of dialog exchanged between Ben and Locke after it is revealed that Ben is an Other?
Locke pressed Ben on the question of “did you press the button [during the lockdown]?” Ben’s reply was roughly “no, and the numbers just rewound to 108…nothing happened.” Ben’s intent seems to have been to sow a seed of doubt in Locke. Thus, resulting in Locke want to ignore the button and cause the whole electromagnetic meltdown (that we saw bits of at the end of season 2) to reach their ultimate crescendo. I propose that this was the result that Ben intended…but it is not what he got.
Early in the first pod of season 3, Ben becomes aware of Desmond’s boat. If I recall correctly, he acts as if this were completely new and unplanned-for information. It follows from this reaction that he probably did not factor Desmond into any of his evil evil calculations and manipulations.
Consider how season 2 would’ve ended sans Desmond. In the event that Locke could incapacitate Eko, we would’ve seen the magnetic chaos rise and rise as Locke stood around hopelessly crying “I was wrong” as his world came to an end inside of a huge underground MRI machine.
It is Desmond who introduces a third option (press button, do not press button, abort) to the mix. A third option that I propose that Ben did not consider. When Ben looks to the purple sky at the conclusion of season 2, he does not do so with a smile on his face, but more of a hidden “well crap, that’s not what was supposed to happen” look. The purple sky wreaked havok on the Others’ communications and has other very bad consequences for everybody on the island. For a lifetime-inhabitant of the island, I don’t think that’s what Ben wanted.
So what was the point of Ben’s original plan?