Island Trinity: Jacob, Man in Black, Christian Shepherd by Zonker

Start with what actually happened and assume that was Jacob's plan all along, then work backwards.

1.1. Man in Black could only be killed by first un-plugging the island. OK.
1.2. No one except Desmond could survive the EM radiation at the heart of the island when it was burning at full force. (Assume Jack only survived as long as he did because he was re-booting the island light... it took a while to get it up to full intensity from its startup).
1.3. So Desmond needed to be dosed with an EM jolt to be effective as Jacob's weapon. Hence the Swan Station implosion back in Season 2.
1.4. So Jacob sent those dreams to Locke in Season 1 to lead him to first find the hatch, and then to lose his faith in button-pushing and therefore cause the failsafe to be activated. Perhaps Jacob was ok with either Desmond or Locke becoming his weapon.
1.5. So Jacob influenced Dharma to build in the failsafe system to the Swan Station. Arguably that was the reason for the 108 minute countdown: over the years it charged whatever system eventually powered up Desmond when the failsafe was activated.
1.6. So arguably, Jacob engineered the Incident, maybe going so far as to flash Jack, Kate, Sayid, etc. back to the 1970s to trigger the Incident and influence the building of the Swan Station in such a way as to eventually power up Desmond.


1.7. So arguably, Jacob brought Dharma to the island in the first place so they would build the Swan Station and eventually produce someone who would activate the failsafe and be useful as a weapon. Possibly Jacob thought Dharma could produce a candidate as well as a weapon for him.
1.8. So Eloise Hawking was acting on Jacob's behalf when she kept Desmond stay on track, and when she helped the Ajira 316 crew back to the island (they were needed to trigger the Incident, etc.)
1.9. Built in to this is an assumption that Jacob was actually a step ahead of the MIB. He knew or thought it likely that the MIB would use Locke's corpse to motivate Ben to kill him. And just like Mother, (who said "Thank you" when she was killed), Jacob was ok with dying as long as he had some belief that the island would continue to be protected, and that through his death, the MIB would be defeated.
1.10. How Jacob was a step ahead of MIB is an area of pure speculation... but try this on for size: What if like Desmond, Jacob's many years on the island gave him some limited precog abilities? So sometime prior to the 1970s he foresaw a flash of the Oceanic 815 passengers coming within range of the island in 2004, then used the Lighthouse to identify a couple dozen potential candidates from the Oceanic 815 passenger list. Beginning in the 1970s, he travelled off island to touch his candidates, who would later become 815 passengers. Maybe by that point Jacob had become disillusioned that either his Others or the Dharma folks would ever produce a suitable candidate.

Next: similar tracing the Man in Black's plan

The extent of the MIB plan depends on some crucial pieces of information not at all obvious (at least to me). Seems like we need to first determine whether every appearance of Christian Shepherd on the island was the MIB. I'm going to say No... even though that causes some other problems.
To be clear, I do think MIB appeared as Christian to Jack in the early episodes, and to Claire at some point to gain her trust. But I also think at least some of the appearances are of actual ghost-Christian on the island.
Reasons:
2.1. In the Lost universe, ghosts are real. Miles actually speaks to them. We first thought Hurley was going crazy when he saw Charlie in the post Oceanic 6 episodes. But now we know Hurley really did see ghosts, e.g. Michael, Jacob, Richard's dead wife. Dead Jacob finally appeared to not only Hurley, but also Jack, Sawyer, Kate at the fireside scene. It is probably futile to try to figure out any rules over who sees which ghosts at any given time, but it seems pretty clear the show is asking us to assume that actual dead people can speak to the living, at least living people with some affinity for the island.
2.2. Christian appeared to Michael on the Freighter ("You can go now.") Smokey apparently cannot travel over water.
2.3. Christian appeared off island to Jack in another of the post-Oceanic 6 segments. Smokey could not leave the island. Now it could have been Jack's drug-induced hallucination, but if so, that would be a cheat.
2.4. Young Ben saw his mother on the island. When he relayed that news to Richard Alpert, it made Richard take note of Ben as someone potentially special. (Likely led the way for Ben eventually becoming an Others leader).
2.5. In one of the "Missing Pieces" webisodes, there is a flashback to the minutes before the opening scene of the pilot episode. Christian tells Vincent the dog "Go wake my son up... he has work to do." Speaking out loud to a dog is arguably silly for anyone but seems particularly out of character for Smokey. Why refer to Jack as "my son" when you're essentially just speaking out loud, with no humans around to try to fool? Also, Jack never really worked to further the MIB's plans, as far as we can tell.
2.6. This one has always bugged me, but I haven't seen anyone else similarly bothered by it: When John Locke encounters Christian at the bottom of the well, near the frozen donkey wheel, this is a time flash to the ancient past. Why would Smokey be flashing to the past along with the Losties? If he did, would he not eventually wind up back in the 1970s with Sawyer, Jin, Juliet, etc. rather than waiting for the arrival of Locke's corpse on Ajira 316 and keeping crazy Claire company in the jungle? Again, this version of Christian tells Locke: "Say hello to my son." Why would Smokey say that? It seems designed to lure Jack back to the island-- and it is not clear why Smokey would want more of Jacob's candidates running around getting in the way of his plans. The candidates don't really present a problem for MIB, as long as they are off-island do they?
So, I'd argue all the above appearances were of the real ghost of Christian Shepherd, made visible by the power of the island. Since Christian says the sideways afterlife exists outside of time, we can assume there would be no problem for his ghost to intercept Locke at any point in Locke's time travels. Now there is the implication from all this that ghost Christian is willingly sending Locke to his death, but maybe once you're a ghost, that's not so much of a big deal!

Where this leaves us is a problem trying to decide which version of Christian first appeared with Claire to Locke in Jacob's cabin
OK, if you buy my above reasoning for at least some of the Christian appearances being an actual ghost of Jack's dad rather than manifestations of the Man in Black, then it seems any Christian appearances are fair game to ask... who was that, really?
Which brings us to the cabin.
I'm going to go out on a limb and say that was not Smokey, but instead the actual ghost of Christian Shepherd who spoke to Locke. This version of Christian told Locke to move the island, and then later when Locke meets Christian at the bottom of the well, that version of Christian also references the earlier meeting, chiding Locke for instead letting Ben move the island, "since when has listening to Ben gotten you anywhere worth a damn?"
So having said that Christian at the bottom of the well is the ghost of Jack's father, then I pretty much have to say that is also who is in the cabin. Which means it is pretty likely Claire in the cabin is the future ghost of Claire as well. Consider: this Claire says Aaron is "fine," and "he's where he's supposed to be," which would make sense for a ghost of future Claire to say, but is very different from how crazy on-island Claire behaved regarding Aaron.
I know this business with Claire is a huge stretch, since nowhere else in the show does a ghost co-exist in the same time frame as its living counterpart. I'm guessing this is actually a broken thread in the plotline-- the writers intended to go one way but changed their minds some time between season 4 and 6.
It also leaves a bunch of stuff unresolved about the cabin, such as why Ilana goes looking for Jacob there, and why it was encircled in ash at one point. I don't have any good explanations, and this is one area where I don't think the show has given us enough information to even make intelligent guesses.
Just one other thought-- in one of Locke's dreams Horace claimed to be building the cabin as a getaway for him "and the missus." Seems very odd that the head Dharma guy would build a cabin in the middle of a jungle with smoke monsters and Hostiles running around. Dream Horace said as he was chopping wood that he had been dead for some number of years. What if ghost Horace somehow built this ghost cabin... after he was already dead?

So that brings us to the Man in Black's plan. If we let go (heh) of the idea that every Christian Shepherd on island appearance has to be the MIB, then we can focus down on a subset of all the various plotlines that was actually driven by the MIB's search for a loophole. I'm thinking it is actually pretty simple: Just as Desmond wound up being Jacob's weapon, the actual weapon/loophole for the MIB was not Locke, but Ben. He shaped Ben over the years, but he needed Locke to help drive Ben's resentment, and more importantly to get Ben past Richard Alpert, who was otherwise protecting Jacob from Ben.

Instead of working backwards, I'll lay this theory out in chronological order:
3.1- MIB claims young Ben when Ben is brought to the Temple waters. I think the only reason for the Season 6 Sayid/Temple plotline was to suggest a similar thing happened to Ben. Like with Sayid, Ben didn't literally become a zombie, he always had free will, but he became more suspectible to the MIB's influence. I'm still not sure why the Temple Others let young Ben live, much less made him their leader, but instead tried to exterminate Sayid. Maybe it was a late discovery by Dogen & co. of what happens when the waters are dirty-- in retrospect of what happened to Ben, they now have a better handle on what can go wrong? Another problem is why would Jacob send Sayid via Hurley to the Temple? Again, not sure, maybe Jacob was in the dark, or maybe Mr. Free Will thought Sayid could still choose to be a viable Candidate, even after his dirty-water-dunking. In season 4, when Ben breaks into Widmore's London bedroom, Widmore says "I know what you are, boy" and I think this means that Widmore has figured out Ben is an agent of the Monster, something Ben doesn't yet understand about himself.
3.2- MIB spends the 1980s manipulating both Dharma and the Others to kill each other off, just as apparently he did to all of Jacob's people prior to Richard Alpert's arrival in the 1800s. This manipulation ends with the Purge.
3.3- At some point, Ben is elevated to the Others' leader, probably in reward for his help in the Purge and for exposing Widmore's breaking of the rules. But maybe Jacob has a sense the boy's not quite right, and keeps him from ever meeting him face to face. Richard's role in all this remains a problem-- you'd think once Jacob put Richard into the role of go-between, Jacob would actually use him somewhat effectively in that role. Maybe Ben distracted Richard with various off-island pursuits like we saw in the 3rd season when Richard was recruiting Juliet.
3.4- We saw in Seasons 1 and 2 Locke's dreams, sent via "the island." Later, Ben mentions he used to have dreams. I'm guessing that's how the MIB primarily manipulated Ben-- sending him dreams that Ben interpreted as the will of "the island."
3.5- My view is once Locke landed on the island, and the Others started recognizing him as "Special" (remember Richard had been waiting on someone named "John Locke" to be Jacob's appointed leader since the 1950s time-travel segment), the MIB saw the opportunity to use Locke to really drive home Ben's simmering resentment of Jacob. The MIB used whatever influence he had over Ben to make Ben pre-disposed to kill Locke, first at the mass-Dharma grave, then finally off-island.
3.6- In this view, it wasn't necessary to the MIB's plan that all the time-travel stuff happened. The important point was that Ben was groomed to resent Jacob enough to kill him, that the Others would choose Ben's rival Locke over Ben, and that Locke would be killed and provide an on-island corpse available for the MIB to copy. The other stuff, including the Ben-Widmore feud, and the time-travel interruptions were outside the MIB's plan. Some of that stuff (Alex's death) the MIB was able to exploit; other stuff (Locke & Ben going off-island) were obstacles.
3.7- So the MIB end game could have been activated any time when
a) Ben was sufficiently resentful
b) Someone else (in this case Locke) was recognized as the Others' new leader with access to Jacob
c) That someone else was dead and available for the MIB to copy.
It arguably could have happened as early as season 3 if Ben's bullet to Locke's gut had hit a kidney instead of the empty space where Locke's stolen kidney used to be!