>>21272134 (OP)
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a) The Alliance version of Moriarty was, of course, Baal; the Moriarty traveling with the protagonists was the real Moriarty. For the purposes of their plan, Baal and Moriarty found a means to temporarily erase / modify their memories and personalities. Baal took on the appearance and memories of Moriarty, without any knowledge of the ruse or the true nature of the alliance. Likewise, Moriarty reduced himself to nothing but a functional personality with barely any personal memories. The "brainwashing" was designed to undo itself only when certain conditions were fulfilled. That is to say, Moriarty wasn't lying when he said that "somebody" had stolen his name and appearance. More details on this below.

b) The term "Ma-Jin" in the context of "The Phantasmal Alliance of Ma-Jin" refers not to demonized humans / Fiends (Majin), but to "Demons (Ma) and Humans (Jin)." That is to say, the name reflects the accord established between Moriarty (a Human) and Baal (a Demon). Moriarty's motive was to exceed Sherlock Holmes, while Baal's motive was to take revenge for Goetia.

c) Baal has been preparing his revenge for over 3000 years; following Goetia's defeat, he's reformulated himself as an existence of passion, built around a dedication to the cause of taking revenge on Gudako. Specifically, the "motive" underlying his actions is that Gudako is too "normal." If Gudako had been some sort of legendary hero or villain, Baal could've accepted Goetia's defeat at her hands -- but Gudako is a perfectly average human with no particularly outstanding talents. For somebody so "average" to defeat Goetia is to Baal an utterly unacceptable outcome. Thus, unlike Goetia, Baal isn't committed to defeating Gudako for the purpose of destroying the world; he's engaged in a plot to destroy the world for the purpose of killing Gudako.

d) Baal has spent the past 3000 years independently researching methods by which to merge Phantoms and Heroic Spirits to generate hybrids -- a feat considered by Da Vinci to be an impossibility. Ergo, this was not actually a technique developed by Moriarty. Despite qualifying as a Caster, Moriarty was never a magus -- and though he was aware of the Clock Tower, he never liked associating with them.

e) Baal either "anticipated" or "designed" the manifestation of the Shinjuku Singularity; specifically, his plan required the existence of a world in which the Common Sense of Man was inactive. It is due to the inactivity of the Common Sense that the district has an air of "unreality" about it, as if it were a location from out of a story or an urban legend; the laws of science / reality normally implemented by the Common Sense are not in effect, permitting that Baal is able to enact the merging of Phantoms or Heroic Spirits unimpeded. Basically, the entirety of the Shinjuku Singularity has become something like the interior of Araya Souren's magical apartment complex; the Counter Force has abandoned this world.

f) After backstabbing Holmes / doing something with Holmes' Saint Graph, Moriarty explains his real plot: He chose to assist Baal because Shinjuku suits his needs as a stage of confrontation with Holmes. He describes the Domain of Man as a World wherein good is inevitably due to prevail over evil; this is simply how timeline mechanics operate. Within the context of the Domain of Man, the existence known as Moriarty is physically incapable of attaining a victory over Sherlock Holmes -- in accordance with some theory that respondents have an advantage over a party that makes the first move. (Ergo, within their shared history, Holmes never acted against Moriarty until the latter initiated a plot; Holmes could therefore easily dismantle the plot as an interloper. It's easier to destroy than to build.) Moriarty believes this "inevitability" could be described as an action of the Counter Force, in the broad sense.

g) Ergo, to prevail against Holmes, Moriarty would have to be on Holmes' side; he could not be the "first actor" against which Holmes goes on the offensive. The plot was therefore to have Baal serve as bait, while the real Moriarty assists Holmes in his efforts -- with the condition of full memory restoration being Baal's defeat while posing as the Alliance Moriarty. Simply acting or pretending to assist wouldn't be enough to fool Holmes; and so the elimination of memory was mostly complete on both the parts of Baal and Moriarty. While Moriarty assisted in taking down Alliance Moriarty, he was doing so in the conscious belief that he was acting in the service of justice.

h) Emiya Alter was hired by "an unidentified party" to infiltrate the Alliance and assassinate Baal. He was waiting for Baal to reveal himself to act; it's possible that he wasn't able to independently confirm the identity of the Alliance Moriarty prior to the reveal. The identity of Emiya Alter's client is unknown; how he managed to infiltrate the Shinjuku Singularity is unknown.

i) Not really interested in repeating Der Freischutz spoilers. Moriarty explains the aesthetics of his plot: The protagonists (Holmes included) are oriented to hold an advantage over "evil" -- but a disadvantage if their opponent is "good." Thus, if "poison" must be used to fight "poison," it is only fitting that "medicine" be used to fight "medicine." In brainwashing himself, he overwrote his own absence of morality with this in mind.

j) JAlter survived the confrontation with Lobo where she apparently suicided; she dropped into a manhole. She shows up during the final battle, along with the real Dantes and Shakespeare and Andersen. Shakespeare and Andersen summon over 200 fictitious "Great Detective" Phantoms, who lend you their powers during combat (charging your NP, etc.). In response, Moriarty uses the Grail that Baal left him with (which he actually had all along, even when he was traveling with the protagonists) to summon a massive wraith.

k) The "Great Detectives'" collective Noble Phantasm is the "pronouncement of guilt." They ask Gudako to say to Moriarty, "The culprit is you, James Moriarty!" Once these words are spoken, Moriarty is locked into the behavior pattern of the revealed criminal in a detective novel, and summarily defeated. Originally, he was going to launch a (fourth) wave of attack, but he's prevented from doing so due to the Detectives' NP.

l) In the end, Moriarty says that he can't comprehend how he could be defeated; in every possible respect, he and his organization outperform Gudako and her allies. Gudako and Mashu theorize that it's because, having finally experienced what it feels like to act for the side of justice, he too desired that he could enact justice; unconsciously, he desired that justice would prevail. Ultimately, he desired that Gudako could trust in him.

m) Once Bennu manifests in the upper atmosphere, it becomes "impossible" for Gudako to rayshift out of Shinjuku. The outcome of Gudako's death is phenomenally "unavoidable," enforced by the Noble Phantasm of Der Freischutz. However -- possibly because the Noble Phantasm of Der Freischutz is acting on the asteroid -- Emiya-Alter's "Unlimited Lost Works" is capable of shattering the stone. This alone, however, is incapable of saving Shinjuku from the debris. To resolve the threat once and for all, Alter unleashes Excalibur Morgan. As the denial of Gudako's rayshift only concludes when the debris is eliminated, it's likely that Der Freischutz's Noble Phantasm was still in effect following the asteroid's shattering.

n) Dantes mentions right before he vanishes that he was "hired" by "one of Shakespeare's fans" to come and resolve the situation.

o) JAlter has the ability to interfere with Chaldea's transmissions at will. She does so to secretly dance with Gudako just before she vanishes.

p) Sherlock somehow survives whatever it is Moriarty did with his Saint Graph. When Gudako arrives back in 2017, Holmes is somehow there. He informs you that according to records left behind by Baal, three other Demon God Pillars besides Baal survived the confrontation with Goetia. After deciding not to explain to you some other secret he uncovered, he offers his services in falsifying Gudako's information within Chaldea's internal records.

q) Prior to the events of the London Singularity, the Charles Babbage summoned by Makiri Zolgen calculated that even in the event that Goetia's plan fails, the History of Man cannot advance beyond the year 2017; certain "anomalous existences" are due to interfere with the continuation of the Human Order in the condition that Goetia is defeated. To investigate the reasons behind this, Babbage engaged the services of Sherlock Holmes. Holmes elected not to assist the protagonists in their quest during the Incineration beyond giving hints because he judged that the matter could be resolved without his involvement.

r) It's hinted (?) that after the Singularity is resolved, the Hessian Lobo might still exist somewhere within real Shinjuku. Possibly, he's fused with Alter's dog, Gaius II, maybe becoming a DRRR-esque Urban Legend ... (?)