Spoilers from included and/or represented works abound. Please read this fiction carefully.
"Based on the notes we found, I find the Rift Goddess related to this very trial!" Phoenix pointed it out. "We know that Kyoman and KD are created by the Rift Goddess, but check the logs!"
The girl heard the 'KD' initial, and is shook to the core. She didn't seem to react any further other than disbelief.
The log revealed NEST, or rather, NESTS, has been taken by the Rift Goddess, bringing all the remaining members of the organization sans the whoever defected before the fall of NESTS, all to become her servants. Kyoman and 'KD' were created using the same cloning program NESTS possessed, but only Kyoman was successfully converted. The Rift Goddess wanted to capture 'KD', so she used Krizalid straight from a dream match as a bait, and crammed him alongside all the forgings shown in the trial right now all towards the Khura'in court, taking advantage of the court abilities of lawyers and prosecutors alike. All of this doubled as one of the many contingency plans in case the Memory Tunnels failed to convert everyone (which it did fail).
Turns out all the forgings was created to lure the lawyers and prosecutors into exposing the alliance and 'KD' to the Rift Goddess. 'KD' defection is thus what led to the trial in the first place.
"All the forgery be damned!" Phoenix concluded. "Nahida proved that this trial is a dud!"
"Actually, I also deduced all the other proofs to be forged, and they'd lead Krizalid to what would be a guilty verdict." Edgeworth noted. "Wright has a point. This trial is ridiculous. If the real life law gets this, everybody in court would panic."
"I cannot see them lying right now." Apollo Justice noticed. "Mr. Wright and Mr. Edgeworth is right. That leaves Krizalid a not guilty verdict. You can say things now, KD!"
'KD' sighed. "Fine then. I'll tell you. I am the freeze-burner K/Diamond, or KD for short, the unity of K the flame, and Diamond, the Anti-K', and..."
Note: K/Diamond pronounced 'K the Diamond'. She has K's and Kula's DNA, specifically from coming procedure grafted to the normal [REDACTED]...
flashback*
"She has much potential, but why'd she escape!?" Kyoman vented his disappointment.
"I'm sorry to have let your sister get away." The Rift Goddess (as Genjitsu-no-Omnia) sighed. "But good job on burning all those Archons."
"If only she could freeze them all first..." Kyoman gets it.
The conversation was overheard by KD and Nameless, the one clone taken Kyo and K', and one of the DNA 'donor' to Kyoman.
"Damn it, if only your brother could realize Genjitsu-no-Omnia's wrongs..." Nameless lamented.
Not long after, the Rift Goddess sensed Nameless...
"K/Diamond, run!" Nameless has KD escape.
KD managed to escape, though the Rift Goddess spotted her and brutally beheaded Nameless.
"Bullshit. That's what you get for sympathizing with having someone defecting my empire." The Rift Goddess then takes the ice glove, which contains Isolde - specifically her soul - and...
The Rift Goddess gave the ice glove to Kyoman, and is told to take care of the Fatui Harbingers, and kidnap Nahida and anyone working for that, in case the God-Scientist/that Singularity dies.
"Thank you. I'll serve you for your ambition." Kyoman's made the servant.
Back to the present...
Nahida appeared, and completely confirmed what KD just said.
"Now, you have to stop the trial altogether." Nahida told everyone. "Also, the courtroom will have been engulfed in flame, so that's even more reason to stop."
"Bailiff! Bring everyone out of the court, now!" Dr. Manhattan then teleported away. "Also, not guilty!"
"See? I'm not the one this time!" Krizalid laughed.
Krizalid got captured by the Foundation, and is kicked out. At this point, flames entered the interior. Everyone quickly left the room altogether, leaving it to burn away and collapse. Maya takes advantage and channeled her spirit energy to spot the Rift Goddess.
And it worked, even though the courtroom is completely burnt out. Not only everyone in court survived, but Maya found out just what kind of trial it is.
"Yes, it's indeed a trap." Maya confirmed. "Nick, we're saved, and exposed the Rift Goddess again!"
"Phew! Thanks goodness we pulled the logs and K/Diamond confessed!" Phoenix is relieved.
"The trial has been stopped. Krizalid not guilty." Dr. Manhattan concluded.
Krizalid cried like a baby.
"C'mon, you're defended." K' told Krizalid. "We normally would beat you up, but since we're in the reality mess together..."
Kyo Kusanagi and the rest of the Sephirah arrived.
"Sorry, the trial's a dud." Miles Edgeworth responded.
"Oh, Mr. Mitsurugi... I see..." Kyo Kusanagi responded back.
"Guys!" Malkuth saw Sephirah coming.
"What's with the trial?" Hod wondered it. "What's the verdict?"
"Krizalid not guilty, but the trial's a dud." Phoenix Wright then explained everything that happened in the trial.
"Oh, I see, Mr. Naruhodo..." Kyo Kusanagi replied. "And Ms. Ayasato, why is your eyes like the Rift Goddess's?"
"I'm channeling my spirit power again, to let me-" Suddenly, Maya coughs blood.
"Oh no! Maya Fey's coughing blood!" The Paradigm noticed.
"The Rift Goddess forged the entire trial, with intention of bringing K/Diamond..." Maya Fey then stops her channeling, to prevent further strain. "I'm tired, Nick..."
"She channeled the spirit power through the Rift Goddess twice in a row, and now she's...!" The Imagined realized.
"She needs to take a break." Netzach concluded. "Maybe she can retreat now."
"Heal my brother, and have him realize the errors of the psycho!" KD begged.
"Yeah... Let's go. We can't waste our time for remembrance." Hokma then led the way.
Everyone go back to the Material World, which recently has been liberated after the bloody flood. They all settled at the Shinra HQ.
Evening...
"Where... am... I..." Kyoman woke up, completely healed.
"Brother!" KD is yay.
"What... did I... do...?" Kyoman is fuzzy.
Malkuth quickly explained all his deeds when he was serving the Rift Goddess.
"Uhhh... So she's a... psycho?" Kyoman started to figure it out.
"Oh my goodness, it worked!" Malkuth is excited.
Kyoman in tears, remembering how ruthless and evil he was when in servitude to the Rift Goddess.
"My flame, what have I done!?" And he cried hard.
"Don't worry, it's already done with..." KD hugged Kyoman.
"Congratulations on all recovery." Malkuth responded. "I'll go out for a while."
Malkuth left the Shinra HQ, and gathered up with the rest of Sephirah.
"The clones reconciled and realized." Malkuth reported. "It worked!"
"Hah," *sips coffee with his mug* "we are finally free of that NESTS." Chesed is relieved. "What a time to be a-"
"Glad that the clones are on our side now." Tiphereth commented. "This leaves us with the Rift Goddess, the last three crystals, and the Sword of Reality."
The special sword, with Zero Point color, Monado grip and kindred burning blade, appeared in Tiphereth's hand.
"This interesting sword has some interesting implications." Tiphereth holds it. "I wonder how it's made, and what's inside it..."
"Not sure what's with this sword. The Rift Goddess threw it apparently because it... rebelled?" Netzach commented.
"Wakey wakey!" Tiphereth woke it up.
"Why are you calling us?" The voice of Dark Knight and Creator echoed from the sword.
"Whoa!" Tiphereth is surprised. "This sword's alive!"
"What!?" Gebura is surprised. "And... the voices!"
"Who are you?" The voice of Creator asked.
The Sephirah immediately introduced themselves.
"Oh, we know now." The voices understood.
"This sword talks." Yesod noticed. "Maybe we should have a conversation with it."
"Who are you?" Tiphereth asked.
"Good question." The voice of Dark Knight. "Do you know about the Vilmark experiments? Or the Time Gates-"
"You know that much about the... wait a second..." Malkuth sensed something's wrong.
"You... you weren't... saved..." Hod realized. "You were... among the victims..."
flashback to a past cycle*
"I never knew you existed." The Dark Knight while he and the Creator is defending other victims.
A girl who resembles Yan Vismok, but taller and busty and with multicolored eyes.
"Mr. Vismok! You can't!" The Creator cried.
"Your powers are impressive, so-called supplementary warriors." The Rift Goddess (turns out to have possessed Yan) then kills both warriors. "Time Gates, by Cabala, and your style... your powers and abilities is what I needed!"
A dozen of cycles later, the Rift Goddess created the Sword of Reality. Inside that as a pair of souls trapped in the cursed, they both met and befriended Malevolent Entity, Hi-no-Kagutsuchi. Back then, the Rift Goddess fused with that Singularity, the other Dr. Sigurd, and became what's know as Singularity Outbreak.
So the first time the Rift Goddess was using it, the voice from both rift warriors and the Malevolent Entity, alongside all other souls trapped, ended up annoying her, leading to the blade rebelling, preventing the Rift Goddess from reliably unleashing the might of the sword.
"Damn it! Those lowly souls... They kept crashing my sword!"
In the end, at the end of that cycle, the Rift Goddess threw the sword away before breaking the Zero Point.
Back to the present...
"You there were among the recipe for this cursed blade." Malkuth understood.
"I can hear the screams of the Elder Gods, and all kinds of archsages as the sword was used." Dark Knight explained. "They, alongside pretty much all other souls inside this sword, became at peace when the Singularity Outbreak threw it out of the way."
"The Rift Goddess abused you!?" The Sephirah are shocked.
"Therefore, we're glad that you and your alliances are using this very sword responsibly." The Creator thanked. "By the way, all our powers resides in this sword, so you can access any of our powers."
"Who else is trapped?" Tiphereth asked.
"I need to ask one." Yesod suggested himself.
"Hello, I'm Saya, agent of Ouma coming from a past cycle." The older version of the voice from Saya, coming from the sword.
"Saya!?" The Sephirah are surprised. "You aren't the same one as the Saya who's working with us directly!?"
"You know me from another cycle!?" Old Saya is shocked.
Hod quickly explained Saya's involvement in the incidents.
"By the way, you also know about the 101 Embryo Project, right?" Malkuth asked. "To be fair, we saved Kyuju Kyu and Byaku Shin together about... a week ago, in our part, specifically."
"And that those Embryo Project creatures, collectively Tsukumo-101, can be used to merge the worlds in its vicinity." Hod noted. "It's like fulfilling Ouma's original true purpose right off the bat, with chaos at the center of the aftermath."
"Oh my god, this is so interesting!" Old Saya snarked.
The Sephirah recapped everything that happened since the true destruction of the Zero Point, Zero End, from the start of the omniversal genocide up until KD and Kyoman freed and joined.
"I have an idea." Old Saya got it. "Take the Centipex, and have Dimension Fusion Charges!"
"Merge the worlds altogether, to the point so that the light and darkness melts away into and become one!" Old Saya suggested. "Merge into a brand new world!"
"The Rift Goddess will be so pissed off, that you'd know how to-" Old Saya continued-
"Thanks." Hokma thanked. "Please rest in peace, older version of that Saya."
"Ok..." Old Saya is done.
The Sword of Reality stops talking altogether.
"Ok, let's report that to Ouma HQ." Malkuth suggested.
"For our best chance at victory, we have to act with sufficient and appropriate haste." Yesod got up.
The Sephirah stands up, and ran to the coordinates where Ouma HQ is.
The night has arrived. The super island crew spotted the Zero Point again with their techs.
"Just as suspected. The Zero Point has been relocated back into its centering, right on the amalgamated reality." Mecha Strike Sentry confirmed.
"Huh. I wonder what the Rift Goddess is doing to the Zero Point." Agent Jones noted. "Besides, I'm now longer in a ghost, now I'm back as a human of sort."
"Glad you're back to life." The Herald responded.
"Actually, I'm watching you." Agent Jones told the Herald. "Now deal with it and get to job already."
"I can sense... some black Aku-creature approaching us." Mecha Strike Sentinel sensed something.
"Uh oh." All figured it out.
Bill Cipher appeared. He's covered in Aku black substance, complete with fire on top of the eyebrow.
"Aku-Cipher!" The Foundation realized.
"Hello, Strangers of the Crossing!" Aku-Cipher greeted.
Wasting no time, the Seven shot Aku-Cipher. It isn't very effective.
"Ugh!" The Order is frustrated.
Aku-Cipher then holds the Twins together.
"Imagined! Order!" The Foundation noticed.
The Herald threw Chrome onto Aku-Cipher, causing him to get blindsided, saving the Twins.
"Thanks, you monster!" The Imagined thanked the Herald.
Suddenly, Jones got the message. It says: "Seven, IO, Last! Please go to the Ouma HQ! We have something to show you all!"
"Guys, tell Geno, the Queen, and some of the Loopers to go alongside us!" Agent Jones shouted.
"Ok." The Foundation then called.
The Seven also ran away alongside Jones. The Herald pinned Aku-Cipher away with Chrome wolves, then ran away.
"Destination: Ouma HQ!" The Paradigm ran.
The Seven and others to go to Ouma HQ. Geno and the Cube Queen received the call, and they responded by going to the same HQ as well. Some Loopers also ran towards Ouma HQ.
Meanwhile, at Ouma HQ...
"We're all going to replicate the Song of Rifts setting, redoing my plans!?" Saya is shocked.
"Are you serious!?" Reiji questioned the plan.
"The older version of Saya told us to." Yesod replied. "And no, we're not kidding. If it's for our best chances at victory and survival, just do it."
"The sword said that's the best way." Hod replied.
"Ugh, fine!" Xiaomu conceded. "So, why not make that a quick setup?"
"Okay then! Do it, everyone!" Mii shouted. "Gather the entire agency and the Oros Phlox, now!"