What was the plan? What was the end desired result? Was it a new IS "world" order centered around the WOB protectorate with all the houses broken?
The original plan revolved around the Third Peaceful Transfer. The First was the original Star League. The Second was the recreation of the Star League in the face of the Clan threat. The Third would've been the elevation of the Word of Blake - or, as they preferred to be called, the True ComStar - to an equal member of the Star League Council. They did not initially intend on the Jihad (by the way, that wasn't their name for the conflict, but was instead a bit of "yellow" journalism). The Word of Blake had meant to unveil the Shadow Divisions as a gift to the SLDF, a powerful force meant to overwhelm the remainder of the Clans. With their forces leading the way to destroy the traitorous SLDF-in-Exile and the Chaos March transformed into a peaceful Protectorate, the Word of Blake would've guided the people of the Successor States forward into a brave new age.
It was not a perfectly rational plan, but that was the idea.
When the Capellan Confederation snubbed the final Whitting Conference, the Word of Blake felt betrayed, but had known it was coming (after all, Sun-Tzu didn't even bother showing up). They had already set plans in motion to punish the Liao state for this insult, which is why the Capellans were hit the hardest in the opening stages of the Jihad. The Steiner-Davions withdrawing from the Star League was, however, unforeseen. This was a sudden shock, especially as the Word had actually given covert assistance to Victor Steiner-Davion (the destruction of Katrina's WarShips right before a major battle, for example). The commanders of the WoB fleets sent to New Avalon and Tharkad - which had been meant as gifts for the two nations to help rebuild after their civil war - over-reacted and chose to lash out angrily. The orbital bombardment of Tharkad led to unintentional tragedy when the shots managed to cause a massive (non-atomic, though it did scatter radioactive fallout) explosion at their primary power plant.
Like many cults, once their prophecies failed the Blakists faced a hard decision: admit that it was all a bunch of BS, or continue to take their anger out at those who had betrayed them. The Blakists struck hard and fast at the three states that caused the failure of the Star League: the Federated Suns, the Capellan Confederation, and the Lyran Alliance. In the Draconis Combine they actually worked against the Black Dragons to help preserve the ruling line (Theodore had been a Star Lord, after all). The Cappies and Davions were pushed to open warfare, especially after the bombardment of Sian and evident death of Sun-Tzu Liao. The Free Worlds League surged across the Lyran border, even as the Protectorate finally went on the offensive to recapture all the old Terran Hegemony worlds. Meanwhile, ComStar was forced out of Rasalhague and horrific weapons of mass destruction were readied for use. The Word might have justified the "Jihad" to themselves by thinking they hadn't started it, but they knew the lengths they'd have to go to even have a hope of winning.
(One side note: the vendetta against Wolf's Dragoons and the scouring of Outreach were not, strictly, events related to the Jihad. The Word had always hated the Dragoons for their Clan origins, and the mercenaries had been working actively to foil their plans in the Chaos March. Even without the Jihad, Outreach would've burned.)
You always have to keep in mind that Thomas Marik - the real one, called the Master by the Manei Domini - was truly insane. His schemes may have borne fruit, had he not hidden them all away. The Word of Blake was so intent on not spoiling the surprise of the Shadow Divisions that they couldn't even hint at their existence, not even when it meant the failure of their prophecies. The institution was too centered around the Master's cult of personality to even consider a different course of action, and the hard core believers - the Manei Domini cyborgs, the Sixth of June saboteurs, etc. - had no problem switching gears when his orders went from "give them gifts" to "punish them all." He was so self-assured of his own correctness that even as Devlin Stone finished conquering the Protectorate, even as the Regulan warheads began falling, the Master viewed it all as the culmination of his prophecies and plans.
The Master thought he'd light the Inner Sphere on fire once his fever dreams were repudiated, and he did...for a time. But instead of the great powers finally destroying themselves in an orgy of violence, the Republic of the Sphere was born. For the first time in centuries the Successor States stopped, looked around, and decided that maybe they could give this "peace" thing a bit of a go. It was all bullshit, of course, as there were several wars during the Republic Era, but nothing like what had come before.
Now, we are left with one final question: who triggered Gray Monday, in 3132? And why? Nobody (outside of the core developers) knows, and maybe that is where we'll find the last act of the Word of Blake.