The Enterprise thereby gets involved in a multiversal enmity between two time traveling characters (Lazarus and Anti-Lazarus), who have duped them into coming to the planet for various reasons of their own purposes. The interesting point about these two fighting men, is that each says that the other is the one that needs to be stopped, and they both want Kirk's sympathies. And each man is disappointed in the crew for not being able to easily realize which one they should trust. Was that why MIB said he was disappointed in the people on the beach, because we silly humans can't figure out which entity to believe and follow?
Both Lazarus men seem to be lying and Kirk can't get to the bottom of it until he goes back down to the planet: "Once there, he meets the other Lazarus, the sane Lazarus, and learns the truth. Anti-Lazarus' people discovered how to pass through the negative magnetic corridor that both connects and protects the two universes. When this happened, Lazarus couldn't bear the knowledge that he had a duplicate, and resolved to destroy his other. He is mad and doesn't care if this causes the death of two universes. Anti-Lazarus and Kirk realize he must be stopped: if Kirk can force Lazarus into the corridor, Anti-Lazarus can hold him there, and Kirk can destroy his spaceship – which will also destroy Anti-Lazarus' spaceship. Access to the corridor will be sealed forever, and both universes will be safe. And two men named Lazarus will be at each others' throats for the remainder of eternity." It reminds of me of how Jacob said that he had an old friend who was tired of him. MIB seems to not be able to stand to exist in the same timespace as Jacob, and has wanted to kill him for a very long time we found out in S5 -- at the same time that we found out that there was an enemy of Jacob.http://tos.trekcore.com/gallery/thumbnails.php?album=53&page=23
Now I'm not saying that our island pals are matter and antimatter and obviously our universe will not cease to exist if they are both in it, because we have seen them together. But we have one seemingly passive and one aggressive entity at odds with each other, and like Kirk we're not sure which one is the benign or malignant one. And MIB doesn't seem to care what will happen to us or our universe, if he kills Jacob. Is this why Widmore and Hawking seem pretty scared? In the end of The Alternative Factor the "good" Lazarus locks himself away in the multiverse corridor with Kirk's help, to save both universes from destruction, where they will fight each other forever. Jacob seems to have already sacrificed himself, will the Losties help Jacob trap MIB in a similar way to "...save us all" as we keep hearing?
A nice synopsis of the ep and screencaps can be found at these two sites: