The plot's status on the wiki page is still more or less accurate as to our current circumstances. I quote:
Kotori directed a mission which placed her vessel directly in open conflict with Black Spiral. The goal was to find evidence that the black ops organization may have been involved in a previous attempt on Empress Himiko's life back when she made an appearance to christen the Y.S.S. Himiko
They found said evidence during a raid on an Ikoi station staffed with Black Spiral personnel, but the ensuing coming of blows cost the crew of the Miharu. Though the cruiser came ahead in the fighting, military police appeared and it was announced that the Ketsurui clan disavowed Kotori's actions, disowning her in the process. To appease the MP forces, Kotori surrendered to arrest, trusting that her crew would present the incriminating evidence at her trial to exonerate her actions.
However, the MP squadron never made it to friendly space: the squadron's ships were found destroyed, with Kotori presumed dead. The crew is now back on Yamatai, trying to piece together clues that some outside factor might have staged Kotori's death - trusting that somehow she is too valuable for the opposition to kill.
Threads 4.0 and 4.1 happen around the time where the Second Battle of Nataria is set, though my narrative sets it up as a campaign which lasted a couple of weeks - the actual event you staged for the Second Battle of Yamatai was probably the final climax of that campaign. 4.2 will be set just after the Second Battle of Nataria. During that period, the mental backups were unavailable and prior backups corrupted - so death was permanent.
In Kotori's absence, Yukari is captain of
Miharu II, which is grounded and undergoing repairs from its previous conflict with Black Spiral.
- My SAINT rear admiral, Celeste, was responsible of keeping tabs on Kotori to keep her contained should her discontent for the Empire prove a threat. (Celeste is a SAINT Elysian archangel Shôshô introduced as Reika's supervisor at the very beginning of the Byakuren plot)
With Kotori out of the picture after being involved in a few major Shadow Viper-related incidents threatening royalty, and two Black Spiral squadrons destroyed for it - Celeste finds herself out of favor and her department is likely to be closed down once the Second Battle of Nataria is resolved. It's hinted that she is soon to be 'honorably discharged' out of the way.
Celeste finds the circumstancial evidence against Kotori shoddy and convenient, and out of a sense of pride for the quality of her work, decides to use her remaining time in office to collaborate with Yukari in order to find out more on what really happened to Kotori.
- The evidence that Black Spiral was involved in the attempt on Empress Himiko's life is compelling, which grounds Black Spiral while the Star Army skirmishes with the Kuvexians are heating up. Taisho Irim, through her underlings, makes is clear that she doesn't appreciate that and tries to damage the evidence against Black Spiral by putting in doubt the crew of the Miharu.
- Miharu defeated two entire squadrons of Plumeria gunships, with survivors reporting she was blinking in-and-out around the battlefield, which allowed it to sink 8 warships without itself being destroyed. Celeste rebuffs the accusations by explaining that the Himiko-class traded a main gun for a powerful electronic warfare package, rebuffing the intent to teardown Miharu for its tech; and anything else yet unexplained is need to know.
- What actually happened was that the Miharu clan reverse-engineered a piece of alien time-altering tech they obtained from Amaya's Gate (near the end of the original Miharu plot). They originally wanted tech that would help them survive null-time space like where the Second Draconian Fleet was trapped (only a fraction was saved), and instead ended up with a ship-sized teleporter which allowed them to save up to 3 locations and instantly teleport to them.
This is how Miharu II actually survived being ambushed by 2 squadrons of Black Spiral Plumeria gunships. They were reluctant to put the tech to the test on a live battlefield for fear of escalating use of time-altering technology or being targeted for what they might potentially be able to do with it. They were left with no choice: not using it meant dying.
Thanks to Celeste covering for them, they narrowly escape Irim's scrutinery. After all, Black Spiral operations are Mishhu-oriented, and there's what might be the deciding campaign with the Kuvexians that's going on. Celeste herself isn't fooled, but based on past heroics from the Miharu crew, decides to turn a blind eye to it.
- Yukari and her staff review the surveyed evidence of the 'crime scene', where a SAINT surveyor ship snapshotted volumetric data on the four destroyed Yui destroyers that had been part of the MP squadron transporting Kotori to Nataria.
- Is it clear they were downed by kuvexian weaponry.
- There is no hyperspace exit trail from the perpetrator
- They were destroyed while in formation. From the killshots in their flank, they were not facing the aggressor at the time they were destroyed.
- It is unknown why they dropped out of fold mid-way to Nataria.
Investigation and computer-assisted renderings eventually reveal that the SAINT surveyor was actually a SMX Xianthrafruglu-class gunship grafted with kuvexian weaponry, which raises the suspicion that the surveyor might have been the perpetrator. This raises an alarm, as this mean this outsider vessel was able to send data to SAINT, that it was somehow vetted through, and that it was then presented to the admiralty as evidence!
- Given the gravity of the security breach and what had been taken for granted on incorrect information, Yukari quickly goes to Celeste to present her evidence. Celeste takes action and schedules a face-to-face meeting with Director Shida to grant Yukari's team broader access to SAINT IT/networking architecture to figure out how the data was allowed to get in and track down the culprit; as well as arrange to have sensor logs from salvage ships whom later came to the scene to recover the wrecks (in hopes that those would have the real answers).
Celeste then leaves to meet with Shida, but perishes when - for some yet unknown reason - her elevator catches fire and burns her down to charred bones. Given the current condition, her apparent murder has permanent consequences.
Thread 4.2 will start with our characters picking up the pieces and trying to move forward despite losing what had probably been their best ally in that investigation.