Draco: If you don't roll credits during the bike ride after Realgam, you roll them during the boat ride after Citadark. If they're after Realgam, Rui's beach cutscene takes place after the credits, and when you load the save file, you're at the table in Gateon; if they're after Citadark, the start of this chapter receives the treatment, and when you load the save file, you're in Agate.
And just for the record; Ardos' Shadow Froslass and Eldes' Shadow Gallade end up in Miror B's missed-list if you didn't Snag them last chapter. #GameplayAndStorySegregation | Nothing else on Citadark Isle is something you cannot get elsewhere in the game, so you're not missing anything completely irreplaceable (which isn't to say you're gonna wanna miss the Rare Candies and PP Maxes).
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Chapter 27: Darkness Returns to Light
Lovrina was waiting on the dock at Gateon Port when the Luxo Cruiser came back. When they pulled up, she watched, shocked, as Rui and Wes dragged Nascour onto the shore; once his feet were on solid ground, he turned away from the boat and found her staring at him.
A smirk rose on his face. "Lovrina."
After a moment, she brought her hand back, and Wes winced as she backhanded the Cipher General hard enough to leave him faceplanting on the dock. Rui noticed that there was still a ring of black around the whites of her eyes, but suspected that didn't have as much to do with the blow as it should have.
"You deserved that one," Wes observed.
Naps climbed onto the deck. "What should we do with him?"
"Take him to Pyrite Town," Rui replied. "Have Chief Sherles deliver him to where they put Evice."
Lovrina looked at them. "Are you sure it's a good idea for a former Admin and a former Peon to walk into the police station?"
Naps shook his head. "Guess that's up to them." He held something out - it was an NFC tag. "Here. Ein wants you to stop by the Under sometime."
"Will do," Wes promised, accepting it.
+x+x+x+
They made sure Nascour's escorts had transportation to Pyrite before they left; once he was on his way, Wes and Rui headed back to Agate. It was rather late by the time they arrived, and Rui took a deep breath of the night air.
"So?"
Wes glanced at her. "What so?"
"Do we go to grandpa and decide what to do with the Manaphy Egg, first?" Rui asked, "or go to the Relic Forest and hope Celebi can heal Lugia?"
"Relic Forest," Wes replied. "If she can purify an XD Pokémon, we should do that fast."
Rui set a hand on the Dusk Ball off her belt. "And if she can't?"
"...One thing at a time, Rui."
They made their way through the cave, finding themselves in the Relic Forest. Rui drew out their remaining Time Flute, and after taking a deep breath, she raised it to her lips and began to play. That beautiful sound flowed through the clearing; as before, the flute began to vanish in her hands as the melody subsided, and a light gathered above the Relic Stone as the Time Traveller appeared in this era once again.
Celebi's wings began to move as she opened her eyes, regarding the two of them. The curiosity of last time was absent; her demeanour was solemn this time, recalling for the purposes she had been summoned before. Rui traded glances with Wes, taking a deep breath; then she seized the Dusk Ball that contained XD001, holding it before her.
The Time Traveller angled her head, seeming surprised that there was only one.
Wes stepped back as Rui threw the Ball forward, Celebi following its arc with her gaze; it landed on the opposite side of the monument, and darkness flooded the clearing as Shadow Lugia appeared there. The Time Traveller cried out at the sight, concerned at the changes that had shrouded the Silver Stormbringer; she soared up towards the Shadow Pokémon, and before it could make to attack, she set her hands upon its chest.
A fearful gasp emerged from Celebi - she knew there was something different, and for a moment Wes feared that she wouldn't be able to unmake it.
Then familiar phantasmal images began to gather from around the clearing. Ephemeral Celebi from across the ages began to converge on Lugia, the power of the Time Traveller surrounding the Pokémon whose heart had been lost. Rui saw the darkness that shrouded Lugia begin to intensify, seeming to flood the clearing as echo after echo continued to gather.
It was then that the Relic Stone began to shine, its light intensifying that of the Time Traveller.
A radiant light seared heavenward from the monument, blinding Rui to the world - and Wes saw the darkness begin to fade from Lugia's feathers. The silvery sheen of its fins began to fade out, leaving them deep purple as its body became brilliant white once again; as the last of the darkness faded, Lugia's eyes opened, no longer bloody red with anger but regarding the clearing peacefully.
The echoes began to fade out around it, and Celebi lowered her hands, drifting backwards - exhausted, but relieved.
Wes breathed a sigh of relief, his body relaxing at last. "You did it," he praised. "Thank you again, Celebi."
Celebi glanced back at them, giving a tired smile; then she closed her eyes, raising her head as she departed once more. Once she had, Lugia lowered its gaze, regarding the trainers standing there.
Rui shook her head. "No."
Lugia seemed surprised.
"No," Wes agreed.
They each took two of the Poké Balls upon Rui's belt, throwing them forward; Raikou, Entei, and Suicune appeared in the clearing, and Ho-Oh floated above. The five legendary Pokémon gathered there regarded one another for a moment before turning back to the Trainers, who were setting their Poké Balls upon the ground.
"Cipher is done," Rui proclaimed. "There's nothing more for you to do. And to carry a legendary Pokémon into battle, when there's nothing on the line but the battle itself? There's no respect in that."
"What Shadow Pokémon remain, we can find and purify ourselves," Wes assured them. "There's no further need for you to accompany us."
They each moved their feet forward, shattering the hinges of the Poké Balls under their heels.
"You can return home."
Entei and Raikou nodded, and then Suicune followed suit; Ho-Oh and Lugia bowed their heads, respecting the trainers that had saved them. Then each of them turned away; the beasts fled into the forest, and the Rainbow Phoenix and Silver Stormbringer soared out of the clearing, departing across the Orrean skies.
+x+x+x+
When they arrived at Eagun's place, intending to carry on a serious discussion, the old trainer insisted they all sleep on it. Wes was grateful for it the next morning. Once they were all awake, they gathered in the living room.
"Well," Beluh mused, "are they done with for good this time?"
"Yeah," Rui confirmed. "Cipher is finished - utterly and completely."
"And Orre will be all the better for it," Eagun expressed. "Thank you both."
Wes smiled before turning his attention to the Egg sitting on the table. "So, what do we do about Manaphy?"
Eagun hummed. "The way I see it, you have two options," he observed. "If you think she might be safer elsewhere, you could make contact with a trainer in another region, and send the Egg to them, trusting them to raise her on your behalf." Then, sitting back. "Or, if you trust yourselves to keep her safe, you could carry her Egg with you, and see her hatch in Orre. The choice is yours."
Rui and Wes exchanged glances; then Rui stepped forward. "I think... we'll raise her here," she insisted.
"Wonderful," Beluh praised. "Do take care with her, Rui."
"I will."
+x+x+x+
A few days later, Wes and Rui made their way down to the Under.
"So," Rui wondered, "where did Ein want us to go?"
Wes drew out the controls for the UFO platform and the NFC tag that Naps had given him. "Well, let's see where else we can go," he observed, touching the tag to the back of the device. After a moment, the screen lit up; the existing Forward, Rightward, and Upward directions were now accompanied by Downward.
Rui narrowed her gaze. "Down...? Into the gorge? What's down there?"
"I guess we'll find out," Wes admitted.
The two of them made their way to the UFO and directed it downward. The descent went a lot longer than they were expecting; after a moment, the platform settled itself into a groove that left it flush with the surface as they stepped out. They seemed to be standing in front of what looked like the entrance to a Colosseum; Wes offered Rui a confused glance before leading the way inside.
Someone was standing behind the counter - a figure with blonde hair who quickly started when he saw them approach. "Wes, Rui!"
Wes blinked on recognizing the voice. "...Naps?"
"Glad you two could make it," Naps greeted. "What do you think?"
"I think we need to know what this place is before we can tell you what we think of it," Rui argued.
Naps chuckled. "Welcome to Deep Colosseum. This place used to be the preferred Colosseum of the Under before the one up above was made, but it's been abandoned for years. Dakim, Venus, Ein, and Lovrina decided to make use of it."
"Make use of it?" Wes echoed. "What for?"
"They've got a little custom battle challenge for you two," Naps explained. "Come on in, and fight 'em in a row, like a Pokémon League. Well, Pokémon Leagues have a Champion, but you get the idea." He shook his head. "Ein figured a real tough challenge might help you guys with whoever's left."
He beckoned to a small binder that was sitting on the counter, a curious Wes made to pick it up as Rui stepped forward. "Are we the only ones who can fight here?"
"Nah," Naps insisted, "anyone who can get down here is welcome to challenge them. But you guys are the ones who need it."
"Sure," Wes mused, "we'll give it a go."
Naps smiled. "Glad to hear it. I'll let them know you're here."
He started inside as Wes opened the binder; the header in here was Ein File 7: Final Atonement.
Citadark Isle has sunk. The island was equipped with a self-destruct mechanism, meant to destroy the facility in the event that authorities discovered its location - but only once all Cipher members had departed. Greevil, in a fit of rage at his defeat and the loss of XD001, commanded Ardos to set it off without regard for himself or any of his underlings. Only Eldes' rapid announcement saved the lives of the peons, most of whom have been apprehended by the authorities.
Lovrina - who had nearly suffered endarkenment - has decided to join us in atonement. There is an abandoned Colosseum beneath the Under, that has long been unused. We will gather there for a private battle challenge, bringing all we have to bear against whoever may find us.
More than any Trainer, I hope that we can assist any Shadow Pokémon that are yet to be purified. Battle with a trusted Trainer forges a bond between Trainer and Pokémon, and reopens the doors to the heart if they should be closed. If Shadow Pokémon are brought to Deep Colosseum, we can assist in the purification process - by providing most challenging battles to forge that bond.
Wes, Rui... I await the day you come to battle us.
+x+x+x+
There wasn't exactly a crowd watching from the stands of Deep Colosseum, yet - but the fights made up for it. The Shadow Pokémon that they'd yet to purify were indeed rehabilitating nicely as they came off the last fight with Lovrina; Wes and Rui bid the former Cipher Admins a thankful farewell and started on their way back towards the UFO.
"Hey, wait up!"
The voice from behind them had Wes turning around as Naps came out of the Colosseum lobby. "Did we miss something?" the Snagger asked.
"Not exactly," Naps insisted. "But... I just wanted to say thanks."
Rui gave him a look. "You mean, for helping with Lovrina?"
"...Kind of," Naps admitted. "It's like she said in Gateon; when we joined Cipher, it wasn't really for anything to do with the group itself. Nascour made her Admin without really caring about what happened to her if she was careless - and she's always been kind of careless. Ein made her protect herself when he was there, but I was scared that one day he wasn't going to be. So, I grabbed the footage of one endarkenment session... and sent it to a random recipient in Team Snagem."
Wes started. "You sent me that message," he realized. "With the video of the Eevee suffering."
Naps nodded. "I wasn't expecting anything like what you did," he admitted. "I just figured you'd slow down the Snagging. Less Snags, less Pokémon to endarken, less time Lovrina spends in the Endarkenment Chamber. But when they stopped receiving new Pokémon to endarken, Lovrina just ended up working on the XD project instead. I thought I'd wasted my time, and just resigned myself to trying to convince her to be safe... until you crushed Nascour and Evice at Realgam. And Cipher started really falling apart."
"You were the crux," Rui observed. "You led to Wes turning on Team Snagem... and that meant he was in Phenac to save me when I got captured for seeing Shadow Pokémon. This whole thing started because you were trying to protect your sister."
"I-I mean..." Naps looked awkward. "You make it sound more impressive than it is. I didn't really do much..."
"I'm not saying you did much," Rui insisted. "But you did what was right - and means a lot more than how much you did."
Naps smiled. "I got lucky," he returned. "I happened to send it to someone else who was willing to do what was right."
Wes smiled back. "Guess we all had our role to play."
Draco: Yes, blowing the Time Flute would still purify a whole party of Shadow Pokémon if the party includes Lugia, but there's a unique cutscene for purifying Shadow Lugia because the Silver Stormbringer got fricked. And I think there would be one for Shadow Mewtwo, because his endarkenment is at least as deep as Lugia's.
After Citadark, you get to decide what to do with the Manaphy Egg. If you want to send that to a Trainer in Hoenn or Kalos, they can receive it as a Mystery Gift. Alternatively, you can choose to hatch it in Orre, whereupon it's treated like a normal Pokémon Egg. If the Manaphy Egg is in your party, Wes or Rui - whoever is not wearing the Snag Machine - will be visibly carrying the case outside of battles. For the story, I'm naturally having them choose to hatch it in Orre.
And for my readers of Kingdoms Unknown: no tears, Rui knows a beach.
So, there's this old geezer in the Under, near the herb shop, who drops his dentures in the gorge. You can't get those until the post-game, when you receive downward access for the UFO to take you to Deep Colosseum entrance. Upon getting his teeth back, the man gives you leftward access, allowing you to get at a small platform with a single item.
In the original Colosseum, that item was an Amulet Coin, and there are not words for how frustrated I was. That is not something that should be unavailable until the post-game, especially with how tight your wallet is in Orre. In the pseudo-remake, it would be the third Time Flute instead.
Deep Colosseum itself does not run a proper battle challenge, so Miror B. and his flunkies won't appear there. Instead, the 'battle challenge' at Deep is a gauntlet of rematches with the Atoners. A little bonus dialogue, and a hardcore #BossRush for those who want it - but it's not necessary if you're just trying to Snag 'em all. Naps' dialogue at the end happens when you leave the lobby, regardless of whether you took the challenge or not.