Kushiel's Legacy/WMG

Anafiel Delunay Was Secretly Behind Everything.
Having trained Phedre as well as he could with tutors and clients, the ever-subtle Delunay faked his own death, then moved behind the scenes to force Phedre into ever more complex situations, slowly making her into the perfect subject for both rallying a revolution and channeling the wills of several gods. He assumed that House Courcel would eventually turn on her as it had on him (all that loyalty to Ysandre was but a facade to gather allies), and she would then be forced to overthrow it, by sheer weight of her many followers. When that proved unlikely to ever happen, Delunay began molding Imriel instead...

Alcuin Was Secretly Behind Everything.
Who better to be a perpetually-hidden villain than the greatest spy we ever met? Alcuin spent every day of his life since the Skaldi destroyed his villiage thinking of who all had wronged him (the realm that let his father die, Delunay for leaving him the dark so long, the Skaldi for all they had killed, Phedre for actually having friends she loved and trusted, and Terre D'Ange itself for so disappointing him), and how to be avenged. First, he began making secret trips to Skaldia, where he (known there as Kilberhaar - note that D'Aiglemort confesses to working with Mellisande against the Crown, but never to working directly with the Skaldi) made secret alliances, maneuvering them towards war. When Delunay suspected, he had the man killed, and then faed his own death for safety. After that, the war proceeded apace, with Alcuin expecting his trump card of De Mohrban arriving at the last minute to send the Skaldi into a tactical retreat which would land them all on top of D'Aiglemort, forcing them to leave Terre D'Ange in disarray, but this was never needed as Phedre turned the tide a couple of days before Alcuin's plans required (he was holding out for an opening to have Ysandre killed "by a stray arrow").Still, the Skaldi had been dealt a blow they'd not recover from for decades, and he was mostly pleased with his opening gambit. Next, he went to La Serenissima, where he manipulated events with the intention that Ysandre, Benmedict, and Imriel would all die, leaving a bastard son of Prince Roland who still commanded the love of many in Elua's City in a strong position to take the throne. When Imriel vanished, however, he had to cancel his plans to kill Ysandre until he knew what had become of the boy. In the mean time, he went to a minor tributary of Kebbel-im-Akkad, and began raising a force that could crush Terre D'Ange's gods themselves if he failed to conquer her governments. Eventually, his spies in Terre D'Ange located Imriel, and he moved behind the scenes to have Imriel killed in a way which furthered both of his endgames...

Waldemar Selig Was Secretly Behind Everything.
The Skaldi had found a leader who really thought. Selig was disgusted by his own culture, and wanted to found a new one - not some pale imitation of Terre D'Ange mixed with Skaldi violence, but a real new beginning. He engineered the war with Terre D'Ange to be a failure (relying upon Lodur The One-Eyed for the insight into the future which could make this possible), so as to break the Skaldi of their most needless and violent tendencies. Of course, he had to die for it to work, but he had already given Lodur the instructions for his Thanatos Gambit: Lodur went to La Serenissima, and used a combination of runic magic and research into the gods' true natures at the famous Caerdicci libraries to force Phedre's dreams, Asherat's prophecies, an escape from La Dolorosa, the fate of a god-cursed pirate, the sacred rites of Kriti, and a final showdown between two priests of Cassiel... all of which went to bring about a new policy in La Serenissima much more friendly to new trade alliances with unfamiliar powers, such as the new Skaldic trading towns fostered by Selig while he yet lived. Lodur had two more objectives for his new-found arts of god-twisting: create a force powerful enough to weaken most of the remaining nations, so that Skaldia would stand among them as equals, and get the True Name Of The One God out into the open, so that even he would be vulnerable to the All-Father's powers. With these things accomplished, Selig and Lodur had sown the seeds for Skaldia to rise to the head of the world...

Manoj The Tsingani King Was Secretly Behind Everything.
Why is it forbidden for men to practice the Dromonde despite it clearly not being unique to women (apparently unlike the similar abilities of the Cruithne)? Because men's Dromonde is more prescisely directed: it was never hinted that Hyacinthe's mother could either choose what subjects she saw the future's of, nor that she could somehow alter the outcomes of things, but Hyacinthe does both (the latter occurring when he makes Melisande walk on by at the horse fair). Manoj's line have a great gift for the Dromonde, and Manoj himself is the greatest - he gathered extensive knowledge of future events, which he twisted slowly into the shape he desired, going so far as to trick one of his children into selling another's precious virginity to create one of the pawns he needed. His access to several lesser seers in addition to his own formidable powers gave him the leverage to manipulate every last one of the many prophecies that guided Phedre's journey. His main priority, however, was to get Hyacinthe in love with a skilled and versatile spy/scholar, then make him the new Master Of The Straights (having long since determined the Master's curse). This would force Phedre to travel all across the world (indeed, Manoj used his machinations to send her ever further afield whenever she seemed likely to settle down or get trapped somewhere) looking for the one thing that could both free Hyacinthe and accomplish Manoj's true objective: the True Name Of God. With that in his hands, he would be able to reverse the curse that placed the Tsingani on the Long Road to begin with - he would force God to rule that the Tsingani could settle down wherever they chose, and all other people's of the Earth would forever wander at the Tsingani's sufferance.

Yeshua Ben Yosef Was Secretly Behind Everything.
He secretly hated his half-brother Elua, and set about to unmake Terre D'Ange.
 * Half-Brother? Elua is referred to reapeatedly as "Yeshua's misbegotten son"
 * And while we're at it: Nothing about having the same name as Jesus?
 * Uh, that's because he's pretty explicitly show to BE Jesus. Just using the Yeshua name to go with all the alternate naming conventions.