A Complete Turnabout/WMG

The diversion point was that Morgan Fey was born with strong spiritual powers
Figuring this one out myself...

The Magatama in this timeline wasn't the one given to him by Pearl, but is a different one that Phoenix got from Iris.
Since the Phoenix of that timeline has been in a relationship with another Fey all these years, this would certainly explain why he has it despite the timeline switch...

Prosecutor!Phoenix is the one who tried to poison Damon Gant.
Being a prosecutor working directly under Lana Skye, Phoenix would've known about Gant's corruption, so tried to get him out of the way. He ended up incriminating Mia and Dahlia to get himself off the hook. This explains the Psychlocks Misty saw during that trial, and why Lana would ask Phoenix, "Do you really want to destroy everything you and my sister worked for?" and then resign so easily and tell him to do 'what he thinks is right'. It's Phoenix, not her, who would have to take the fall in the end.

Kay Faraday was trying to spy on Prosecutor!Phoenix in order to expose some corrupt dealings of his.
Seems like the most logical reason she'd be in his car to me.

Tsukasa Oyashiki never hid the body of the IS-7 Incident (Gregory Edgeworth's last case) and caused the alternate timeline
Since she hid the body, she's indirectly responsible for the forgery of evidence, which leds to von Karma's penalty, and then the DL-6 incident. So maybe if Tsukasa never hid the body, the DL 6 Incident never happened.

Characters from Gyakuten Kenji 2 will definitely appear at one point.
Since Gyakuten Kenji 2 has the case that started the DL-6 Incident, Tateyuki Shigaraki (Gregory Edgeworth's former assistant) would probably come to see Miles Edgeworth at one point. Sōta Sarushiro and Manosuke Naitō may also have different lives if the IS-7 Incident was solved differently.
 * Confirmed. Word of God on the fic's Tumblr blog states that Nenilein is definitely including some GK 2 characters and there are some hints in chapter 26 which suggest this could be Tateyuki. "...there is one GK 2 character who will show up in this fanfic and he will play a keyrole. You might be able to identifiy him from a passage in Chapter 26, in fact…"

Ema and Prosecutor!Phoenix are investigating the smuggling ring and it involves the case of
According to the author the smuggling ring is still alive. So maybe Prosecutor!Phoenix sent Ema to look for evidence of the ring and the smugglers found out. So they send a black haired assassin (not Yew because she's dead) to kill Ema and take the evidence since Ema's said ""P-Ph-Phoenix… I-I'm so… s-sorry… th-they took… it…", then framed Lana.

Evil!Pearls is actually Dahlias spirit haunting Phoenix.
Mia even said in chapter 24 that the girl pretending to be Pearl was some kind of malevolent spirit but Mia herself cannot figure out who or what she was. How many vengeful spirit women could be out to mess with Nick's head? It would make sense for it to be Dahlia (or possibly even her mother Morgan Fey), although her motive isn't exactly clear. Maybe she is after him as she has no way of screwing Mia over anymore.

Larry's little cousin 'Lil' who was stuck in the tree in one of Phoenix's dream sequences is really Defense Attorney Lilie Heatherd.
As if there wasn't enough Mind Screw in the plot already. It's extremely possible though, because the author is just that awesome.

Lilie Heatherd is part of the smuggling ring which (as mentioned above) Prosecutor!Phoenix and Ema were investigating.
As Yew is dead in this world the smuggling group need their hands on another Amoral Attorney, in this case Heatherd. (for the record Heather is a type of weedy purple shrub like plant while Yew is a poisinous tree. See a connection?) Being Phoenix's neighbour gives her an ideal chance to be a witness so she can draw attention away from the fact that Ema was killed by a black-haired smuggling group assassin. This means she can paint Lana (Who is still under Gant's control) as guilty while utilizing Dylan's computer genius skills to hack into the security camera files, while using him as a scapegoat if Phoenix begins to suspect them. All the while pretending to be "Lanny's" loyal girlfriend. Bitch.
 * The main case against Lana? No one else could enter the apartment. Phoenix and Edgeworth conclude that the killer hit   in the head because they were weaker than her. Heatherd is almost certainly involved somehow, but I wouldn't put a massive plot twist past the author.

Edgeworth is only dating Dahlia because he suspects she was involved in 'that' case.
Athough we don't know what case they are referring to yet (Maybe the BD-7). Translating the German in chapter 22 Edgeworth and Franziska are dicussing a 'missing person' on the security tape. Franziska accuses Edgeworth of keeping a (female)muderer under protection for years, Maybe under the guise of her being his girlfriend? Maybe he suspects her of being the murderer of  Or maybe I'm just trying to explain away the disturbing Crack Pairing that is Dahlia/Edgey. The author said herself that she doesn't support any pairings that involve Dahlia or Edgeworth and that there are plot-based reasons for everything established.

The Iris that Phoenix met at the courthouse and in Kurain, is actually Dahlia.
The meek 'Dahlia Fey' in prison with Mia is actually Iris, it wouldn't be the first time they'd switched places. Misty Fey did see a girl from her family near Phoenix's apartment. If she's not trying to protect Maya than maybe she's doing what any branch family member should do: Protect the 'Master' at all costs. Phoenix himself even notes that alt!Dahlia was much more like her sister: "This Dahlia was different. This Dahlia before me here seemed… scared, weak and fragile… In a way, she reminded me more of Iris than of Dahlia."
 * I also think there's a twin switch going on in some form. Consider these three points. 1, Edgeworth and Phoenix have a conversation about Dahlia dying (or rather bleaching) her hair four times a year to look different from Iris, which is an odd point to give so much detail to. 2, in the letter from Maya to Prosecutor!Phoenix that Phoenix reads, Maya mentions a "hair thing" that he asked her about, saying that it might be better to ask Ema about it instead. This could refer to the way Dahlia dyes her hair, which would be an important point to consider, if Prosecutor!Phoenix thought there was a twin switch going on between his girlfriend and her sister. And it could link into the third thing. 3, Ema's last words, about "the black hair."
 * Other things to consider: Iris has been Master for years, which means... she's the older one? But she also didn't want the position. Did Dahlia possibly want it or at least want to use it? Also, it's Iris's finger prints that are on Nick's door handle, and even twins have different finger prints, but who was the "Iris" that gave the sample they compare the prints to?

Phoenix is becoming the Chessmaster.
Canon!Phoenix clearly entered the world after his disbarment,(hence the Psyche-locks caused by Klavier and Trucy) but before the events of Apollo Justice (as Justice himself caused no locks). Therefor, the events Canon!Phoenix witnesses here will give him the knowledge for the MASON system's impossible leaps of logic. (How did he know Apollo could perceive? He saw it in an alternate universe.) Thus, Phoenix will become his 'all-knowing' self, because he's seen stuff that hasn't happened yet. Alternatively, Prosecutor!Phoenix is in the canon world and either is Chessmaster Hobo Phoenix or is the reason Phoenix lost all his friends.