Larian Studios Forums Baldur's Gate III Baldur's Gate III - Story & Character Discussion The insane timeline of the main plot (do I even need to tell you that it's spoilers?)

The timeline also annoys me a lot, as many things DO NOT MAKE SENSE. Here are my attempts to piece together more information based on what you've written:

In a vault in the Counting House, Gortash's personal documents explain that the Nautiloid was dispatched to the Astral Plane to seize the Prism from Vlaakith, as it was the only device that could possibly disrupt their plan. Before the prism was lost, the Githyanki were simply fighting the Cult of the Absolute. The Emperor is the Mindflayer who tadpoles the protagonists in the introductory cutscene of the game (same armor and head shape), having been sent on the Nautiloid as a thrall to seize the Astral Prism from Vlaakith, which her predecessors had used to imprison Orpheus many, many years ago. The Sharrans caught wind of the Absolute's plan and sent Shadowheart and a covert strike team to steal the Astral Prism from Vlaakith first. Somehow (and it is not explained how) between the opening cinematic and the end of the tutorial, the Emperor gets locked in the Prism, suddenly gaining free will (set free from BOTH the Brain AND the Absolute), and using his power to save the Player Character from hitting the ground during the crash. What makes the most sense now in order is that:
1. Emperor and the Nautiloid successfully stole the Prism from Vlaakith.
2. Shadowheart and the Sharrans were smuggled aboard the Nautiloid or had plane-hopping technology, and stole the Prism from Emperor.
3. Thrall Emperor caught them, and executed the Sharrans and (later) tadpoled Shadowheart.
4. Thrall Emperor continues to tadpole people as an emergency measure for human cannon fodder while being pursued by Githyanki Dragonriders. At this point he is still a thrall and is trying not to bring the Githyanki straight to the Elder Brain and the Chosen Three. If the Githyanki found the Brain while in the vicinity of the Prism, the Red Dragons would EVISCERATE the Ghaik immediately.
5. As it takes time for the Astral Prism to have effect, eventually Emperor's prolonged exposure to the Astral Prism grants him free will.
6. Lae'zel and the Player Character get tadpoled in the opening cinematic.
7. Suddenly endowed with free will, Emperor investigates the cause, the Prism. He finds a way in and stays there.
8. Dragonriders cause enough damage that you are released from the pod and the tutorial begins. Otherwise, Emperor psionically willed you to be freed from the pod.

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Additionally, the Emperor is apparently Balduran himself, not just any Baldurian Adventurer. Balduran founded the city of Baldur's Gate (though apparently other iterations of Baldur's Gate existed prior-- continuity issues from preexisting Realms lore). Balduran "founded" the city and went missing sometime in the 1000s DR, with Baldur's Gate 1-2 taking place in the late 1300s, and Baldur's Gate 3 taking place in 1492. Moonrise Towers predates Ketheric Thorm's activities, who was active 100 years before Baldur's Gate 3, as a 1993 text indicates "Naernythra Thaloudyn was the holder of the Crescentcoat office, and lived at Moonrise Towers," with no mention of Thorm. The region of Moonrise Towers was, from oldest to youngest:
1. The site of a dormant Illithid Colony that survived from the time of the Illithid Empire. It has a Nautiloid, which means it is very old as those rarely survived from the days of the Empire. It was likely not active, probably remaining dormant and biding its time for a moment to reemerge. This is why Balduran was only tadpoled when he actively sought it out during his adventures. Only the interference of the Absolute and the Dead Three caused it to become active. This particular colony, however, was probably responsible for most Illithid activity in the southwestern Sword Coast. This Mind Flayer colony could be as old as -11,000 DR, but is probably somewhat younger than that.
2. The site of an Ancient Temple for adherents of Shar. These Sharrans were able to build a giant temple, which is abnormal for this goddess. The Temple likely predates the Selunite village that was eventually built over it, but it is possible that the temple was built in secret by members of the community. I prefer the theory that the Temple predates the Selunite village, as keeping such a massive structure a secret sounds absurd.
3. A Selunite community and some Harpers and Heralds move in before the mid-1000s and construct the section of Moonrise Towers visited by Balduran. This community, based on the demographics of the Heralds' associated organizations, were mostly humans and elves. Given Ketheric Thorm is an elf, and is thus VERY long-lived to begin with, he may have been a founding member of this community as a younger man with no renown. *****(SIDENOTE: ISOBEL IS A HALF-ELF. Ketheric went into his relationship with Melodia KNOWING he was going to outlive her and probably their children, and he STILL had a tantrum when the inevitable happened. AND he held Aylin's immortality against her EVEN THOUGH HE ALSO HAD A MUCH LONGER LIFESPAN THAN HIS WIFE AND CHILDREN.)*****
4. The community develops into a full village by the mid-1300s. Sometime between 1367 and 1392, Ketheric becomes the leader of the community. Isobel is probably born in the earlier part of that time.
5. After the death of Ketheric's wife (and, later, Isobel), Ketheric revives the worship of Shar in the area, coming to some kind of arrangement with the goddess. During this time, according to the Mason's documents, Moonrise Towers underwent further construction, likely for military purposes. In the late 1300s, Ketheric builds a NEW Sharran temple (The upper level of the Grymforge) on top of the old one. Sometime in the 1400s, Ketheric initially wins the war against the Harpers and Druids (or comes very close to it), only for Orthon Yurgir and a Devil Army to ravage his forces in the final moment. Finally, the Harpers seal Ketheric in the Thorm Mausoleum in the 1400s. The Shadowcurse is released.

It is also possible, based on Ketheric's brother Malus and the existence of (elven) Thorm corpses in the Mausoleum, that the Thorms were ALWAYS Sharrans (Ketheric's ancestors being the builders of the first Sharran Temple), and Ketheric renounced his secret faith for Melodia, only to relapse into the arms of the goddess of loss when his wife died.

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The Dead Three were dead between 1358 and 1482, give or take a few years in either direction, as a result of the Time of Troubles. This means that Balthazar could only be an active Myrkulite Necromancer 10 years before Baldur's Gate 3 AT THE EARLIEST. This gives exactly 10 years AT MOST for the ENTIRE conspiracy of the Absolute to be set up. 1482 is also the year Gortash sold Karlach to Zariel. So, your timeline sounds mostly correct. In order:
1. Gortash makes a deal with Bane and befriends Durge (early 1482).
2. Gortash sells Karlach to Zariel for infernal engine purposes (mid-late 1482).
3. At some point, he discovers information about the Crown of Karsus and the Illithid Colony beneath Moonrise Towers.
4. To get someone with familiarity with Moonrise Towers, the Shadowcursed Lands, and military affairs, Gortash and Durge task the Myrkulite Necromancer Balthazar to resurrect Ketheric. He only cooperates in exchange for Isobel's resurrection. Otherwise, he was never dead and was merely sealed in the Mausoleum, agreeing to cooperate in exchange for his daughter's resurrection.
5. For added security to his part of the deal, Myrkul (through Balthazar) devises a trap for Ketheric and Balthazar to set upon Aylin so Myrkul's champion could be immortal. How an apostate Ketheric and heretic Balthazar imprisoned Aylin in Shar's portion of the Shadowfell is beyond me. The Daughter of Selune with lawful stupid Paladin-Brain was probably lured by rumors of a revived Sharran Chosen. Balthazar's Soul Cage magic probably comes straight from Myrkul himself.
6. The rest of the plan proceeds as usual.

The objective of the Dead Three was not to be worshiped or to acquire souls, as the nature of the Mind Flayers negates these benefits. Given the Dead Three are quasi-divine beings after the Second Sundering, they chose interference in the mundane over the rest of their divine powers. I believe the Dead Three were building an impossibly massive army while simultaneously draining other gods of souls and worship. The purpose of building a powerful army in the Realms while also weakening all other Gods was to recover enough artifacts and capabilities to ascend to Greater Godhood while maintaining full control over the Realms. Recall that despite Ao declaring none would ascend to Godhood without his explicit approval after the Second Sundering, Gale can still use Karsus' Artifacts to ascend. If the Absolute hit a critical mass, it would be able to plane-hop to deny the Greater Gods ANY worshipers. At the same time, the Dead Three would use Karsus' Artifacts, Illithid capabilities, and other things they found to "build" a fully Ascended God out of Karsite and Far Realm materials (and potentially materials from the future, as this Illithid being would be able to assimilate all of the remnants of the Illithid Empire as well). Given all cosmologies are threatened by the same Far Realm, it stands to reason that components of this Divine Abomination would be beyond the control of Ao. I mention Ao because he's the reason the Dead Three died in the first place, and there are few beings quite as petty as the Dead Three. They would definitely want a contingency against the guy that basically killed them last time. Once this Divine Abomination of Karsite and Far Realm essence was completed and the Greater Gods were fully weakened and unable to intervene due to the post-Sundering rules, the Absolute would simply "eat" the other Gods, probably starting with Cyric. The motivations of the Dead Three are revenge and power: Revenge against fate, and the power to control it. In light of this particular motive, Jergal probably refers to Ao when he first meets the player. If BOTH Jergal and Ao are omniscient, then they probably formed an unsteady alliance to stop the Dead Three in light of their mutual interest: Fate spinning along as it should.

Of course, one can argue that Bane just wanted to rule everything, and Bhaal just wanted to kill. But these motives do not explain Myrkul's involvement. I think it makes very little sense for these gods to take on such extraordinary risks and efforts for their own amusement, while also denying themselves worship and souls. As Withers notes, Mindflayers do not have souls, and mind-controlled worship does not endow Gods with greater powers. If Myrkul was not getting souls or worship, and cared little for tyranny or murder, then he needed an even greater motive, being the second strongest of the Dead Three (after Bane).