We're gonna need to look at Elicia's side of the story starting at when she arrives at the Pokémon World. It'd hard(er) to follow if I didn't include her.
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...
[The battle has ended, and some others arrive; Al, Adam, Sengoku, Surge, and Hreine. With the extra help, they are able to support Celebi, Tails, Mew, and Knuckles back to the Capricorn-2, as well as the Time Gear and the Master Emerald, very uncertain of Mewtwo's, Eggman's, and Ginsengaar's fates. Knuckles suffered a strange transformation due to Eggman's energetic blast, empowered by Mewtwo in the first place. His appearance is entirely different, almost opposing his original. He has become Vulpix. As for Cruce, he was reported to have been sleeping in the sick bay of the Capricorn-2, which he still is. Little does everyone know that he now rests his shape-shifting body for a different reason. Despite this, the large group returns all the way back to the aircraft. Derrick, Hreine, and Surge bring it into the sky, and it flies off... ]
M O B I U S
~~Central City~~

[The Capricorn-2 has landed in the street of Central City... All is still. The hatchet falls to the ground... Stream and Sengoku are the first to be seen coming out.]
Stream: ...Wow... Quiet ride home... Quiet city.
Sengoku: The calm after the storm, I guess...
Stream: Yeah...]] [Looks up and spots a figure atop one of the buildings.. It is a dark colored being... A long black dress can be made out.] Uhh... [Backs up, nervously.]
Sengoku: [Notices Stream's fear.] What? What're you looking at? [Rushes to Stream, and glances at the very same figure.] Oh no...
[This figure leaps from the building, on to the ground directly in front of Sengoku and Stream. The two back up nervously.]
Stream: I-uh, we-we-we h-haven't d-d-d-done an-anything!! P-please!! D-don't do what you d-d-d-did to me in thae past!!
Sengoku: We promise!! Our hands are clean, Equinox!!
Equinox: [She is a black fox Mobian, very beautiful in appearance, though beauty is often the sign of danger in nature...] How interesting it is to find you, Team Sphere, out here... Are there others with you?
Stream: Y-yeah! Sonic's friend's are with us... But, they've... Um...
Equinox: Sonic? His friends? Well, even more convenient...
Sengoku: Equinox... It's not like you to show yourself in these sort of areas... What's the occasion?
Equinox: ...I am searching for someone...
[By now, Amy, Al, Adam, and Surge can be seen exiting the ship, but Equinox still remains...]
Stream: This really isn't like you at all... Usually I'd expect you to like teleport out of here...
Equinox: Listen... This is not something I would normally do, practically ever... But... I need your help...
Stream: [Steps back a bit at this.] You... You need our help?
Equinox: Yes... These conditions call for that exactly... [She looks down, depressed.]
[The others notice this...]
Surge: What ther--?! Equinox!? Stream, Sengoku, get away from there!!
Sengoku: Surge, don't worry... It's fine.
Surge: [Approaches.] ...Hmm? Wait a sec... This is definitely a lot different from our previous conflicts...
Equinox: Indeed it is, Surge... [Closes her eyes and sighs.]
Surge: [Lost in thought at this reaction.] Is... Is something wrong...?
Equinox: Please... I have a request... Can you bring everyone who is in that ship out here...?
Surge: ...They're all coming out... [Turns around, spotting Rouge, Uhalo, and Lucario exiting the ship.] I see some others right now. A few are injured, so they can't go anywhere...
[Al, Adam, and Amy approach the scene.]
Amy: What's going on?
Sengoku: So quick after the last...
Surge: We have another dilemma on our hands everyone...
Al: Another? Urk... S-sorry guys... I'm getting pretty tired...
Adam: Yeah, me too... I can't keep up with you all yet...
Surge: It's alright... From what I've gathered so far, the Time Gear we retrieved holds your world's power, and will enable you to return to your world safely.]
Al: Really? Cool!!
Surge: And hey, you guys kept up nicely! Your work back in the jungle was really good, so don't think you're not at our level.
Adam: Thanks!
Lucario: [Approaches.] Hmm, I overheard... It seems our time here has come to an end... Mewtwo has been defeated, and the Time Gear has been retrieved... Mission completed.
Al: So I guess that means we really are returning?
Lucario: Yes. I'm sure the guild is worried about you two. And I must return Mew to his world... From what I gather, he is needed there desperately. I will go get him.
Adam: I guess this is goodbye...
...
Al: It was nice getting to meet you all.
Surge: Hey, it was nice to journey along you two! And who knows? We may get to see each other sometime in the future.
Al: Yeah! That's true!
Amy: Let's all keep our hopes up that we have a good future to begin with!
[Rouge approaches.]
Rouge: So I take it you two are saying goodbye?
Al: Yep. We're about to leave.
Rouge: Well, I hope you have a good trip back home. We may get to see each other again if something like this happens. I don't doubt that, believe me.
Adam: Just like Amy said, let's keep our hopes up.
...
[Lucario, holding Mew tightly, exits the ship. Mew seems to have a grip on the Time Gear...]
Lucario: I apologize for making this so sudden... But we must return quickly.
Al: Don't worry, we understand... I just wish we could say goodbye to Tails and Chris...
Surge: When they wake up, we'll tell them.
Al: Thank you Surge!
Adam: [Seems intrigued by the Time Gear...]
...
[The Time Gear begins to shine more intensely.]
Lucario: [Turns to Surge.] Surge... tell Chris I said good luck... Tell everyone that I'm sorry for leaving so suddenly...
Surge: Will do... We'll miss you all... Good luck.
Al: Thanks! Bye everyone!
Amy: See you another time! Hopefully soon!
[The Time Gear engulfs the four in a bright light...]
Equinox: [Gasps. Quietly.] This light... Oh, I sense his presence... No wonder! Now I understand... He was not in this world... [Out loud.] Chaos Control!!
Stream: What!?
Rouge: Hm!?
[Equinox bursts in warp speed toward the Time Gear's light. She vanishes just as it does... This happens in less than a fracture of a second to everyone else...]
Stream: [Speechless.] ...Wh...?...
Sengoku: What was that!?
Surge: She... She went into their world...
Stream: Now that's the Equinox I know... So unpredictable...
Surge: Well dude, at least she didn't--
Stream: NO! She didn't!! Heheheh...heh...
Rouge: So that was Equinox... That was the one that Shadow mentioned... Even she has the power to "Control Chaos" ...
Surge: She must've sensed him or something... I couldn't really make out what she was whispering before she warped in...
Amy: Wait... If that girl was looking for Shadow, and she went into that portal... Doesn't that mean...?
Rouge: Shadow must be in that world...
Amy: But... how?
Sengoku: Mewtwo? Dr. Eggman?
Stream: 'Has to be one of them... Mewtwo had that Time Gear thingy before, so he must've used it's energy to get him out of the way...
Rouge: Shadow puts up a nasty fight if anyone gets in his way and refuses to move... It's no wonder Mewtwo wouldn't fight him, and just sent him to the other world...
[Derrick and Hreine dash out of the aircraft.]
Hreine: What happened!? What was that flash!?
Surge: You two just missed it... Lucario and his friends just left... Al and Adam were tired, and the other two had to be at their world... Guess who went with them...?
Derrick: ...Who...Who could've...?
Stream: [Coughs nervously, mumbling something in the cough.] ...
Derrick: ...What!? Did she really...?
Sengoku: Yeah... Equinox went into the neighboring world... [Giving his wings a break, he rests over Stream's shoulder.] 'Least you don't have anything to worry about...
Stream: For now, yeah...
...
Amy: Hey...
Derrick: Hmm?
Amy: You guys told me that Sonic took a detour off of Angel Island with Knuckles... I'm a bit worried about them...
Derrick: Erm--they'll be fine! Don't worry.
Amy: And how did others get to Angel Island before us in the first place? That little blue guy, and the red one... They suffered Mewtwo's spell, but who are they really? Friends of yours?
Hreine: Uh, yup! They said they'd rendezvous with us up there!
...
[Uhalo apparently went back into the Capricorn-2, within the sick bay.]
~~Capricorn-2...~~
[Celebi, Tails, Knuckles, and Cruce are unconscious. Worried about them all he watches over their beds... Though his suspicions are greatest around Cruce, Uhalo scans across the room, stopping at Knuckles.]
Uhalo: [To himself.] You fought knowing that this would happen, or something even worse... You protected that Master Emerald with your life... You fought alongside my best friend, Tails... Now I remember... [Out loud in his own words.] Knuckles... Your appearance may have changed, but you're still a good friend. Nothing will change the Knuckles I knew in the past, and the one I know now, even as we undergo these changes...
...
Knuckles: ...[Smirks...]... Sonic? [His voice has gone up, matching his size an form. It is almost unrecognizable.]
Uhalo: Sorry, no S-Sonic here. It's just me, Uhalo.
Knuckles: Sorry... Uhalo, then...You still remember me, huh?
Uhalo: Of course I do... You sacrificed your entire being to keep what is precious to you untouched... Your valiance succeeded in the end, Knuckles.
Knuckles: [Eyes are still closed.] Finally... some good news... Sheesh... I'm feeling pretty messed up right now... If I open my eyes, will I be surprised?
Uhalo: Well... I'll let you be the judge of that.
Knuckles: Right then... [Opens his eyes. At first, he cannot see himself in the position he is laying. He tries to get up, but ends up confused, and falls over into a position where he can see himself.] ... [Sighs.] Yeah... I'm surprised... And a bit embarrassed...
Uhalo: Don't worry. You're not alone...
Knuckles: [Looks over to Tails.] Oh yeah... Did they defeat Dr. Eggman?
Uhalo: They did. And they defeated the one who came to this world and gave Eggman the power to turn you into that.
Knuckles: Shouldn't we all turn back then?
Uhalo: ...It is possible that the source of this is truly elsewhere...
Knuckles: Hm... In the mean time... [Tries to stand up, falling to all fours.] This should be fun...
...
Celebi: ...[Blacked out]...
...
...(What... What I did... What did I do?... It was different than my past manifestations... It converted the Eclipses into Darkness... And that strange person... was it... Cree...? ...I was... also up against the Shades, Naught's closest Minions, again... at least... before I teamed up with him... Ugh... Even still, with that manifestation and six against one...Cree wiped us all out... What the heck was he supposed to be...? I've never faced anyone that powerful before, except... maybe few others... but I was either on my own or with more allies. Still, this power impressed me... Was it... really the true power behind this innocent, little form? Ohh... But I corrupted the Eclipses at that moment... There's no doubt the Phaze Guardians, Starsign Saviors, and even Hideaki himself will notice this... They'll get suspicious... I feel as if I am going to confront them in the future now, all because of my mischievous acts... Because of that, I will have to fight my own friends...
...
But... Isn't that part of the challenge too...?
...)...
...
Knuckles: ...Heh... I guess it's not so bad.
Uhalo: What is that, Knuckles? [Returns his attention to Knuckles.]
Knuckles: [Now sitting up.] This puny thing I am. At least I get the hang of sitting.
Uhalo: Hmhm, I will need to teach you much more than sitting soon.
Knuckles: [Scoffs.] Yeah, yeah... [He looks to the left of his bed, spotting Cruce.] So... who is this guy...?
Uhalo: That human... I do not remember his name, but I feel like I have seen his face elsewhere...
Cruce: [After battling against the six in Cree's form, he received grievous wounds from the pure darkness of Celebi's and the Eclipses' attacks. In the last few moments after using his last resort attack, Celebi had thrust a dark blade into his chest. He was forced to split into hundreds of black bits of matter, all returning to the Capricorn-2 in unison. As they did so, they reformed into Cruce upon this very bed so that none would know who really opposed them.]
Knuckles: ...He must've been a part of somethin' to get himself messed up like that... whatever "that" is.
Uhalo: He suffered great deals of damage from a dark force...
Knuckles: [Turns back to Uhalo.] You can tell?
Uhalo: [Nods.] Yes. I feel it looms in this room as we speak.
...
...
...
[And for others elsewhere...]
...
[A similar ordeal begins...]
...
...
...
THE POKEMON WORLD
~~Treeshroud Forest~~

[Elebi has traveled far... But the forest is shrouded in the darkness of night now, and it is hard to tell where she is going...]
Elebi: ...Hmm... I think I might have to set up camp... It's getting really dark... (Huh...? What's this strange feeling I'm suddenly getting...?)
Carbuncle: (I will bestow upon youa guiding light...)
[The area around Elicia begins to shine brightly, like some sort of lantern.]
Elebi: Oh! Thank you Carbuncle!...Hey... Is it just me, or does something feel suddenly... weirder...? A lot weirder?
Carbuncle: (Hmm... Ah yes... How akward... Two Eclipses have entered this world just now... One is not of this world... Three Eclipses on one world... Strange... Perhaps...)
Elebi: Is something happening that concerns you?
Carbuncle: (...This could quite possibly travel further than I... I had sensed a major disruption in the Eclipses earlier... )
Elebi: In that case, should we hurry and find them?
Carbuncle: (Yes. Perhaps this will tell us more of Chris' whereabouts... Hopefully he is still within this world...)
Elebi: Ok! Time to... Ooh, I've alway wanted to say this! Time to fly! [She soars into the air with a boost of speed at the start, letting the wind blow her the rest of the way...]
...
...
[Elebi, staring at the ground with a birds-eye view, begins to slow down...]
Carbuncle: (Is something the matter, Elicia?)
Elebi: I think someone's down there... It looks like there's two of them.
Carbuncle: (Two unknown figures? Do they look threatening?)
Elebi: Umm... One of them kinda does... It's hard to tell 'cause it's so dark... I'll give them a chance because we seem to be the only ones out here...
Carbuncle: (Even still, be cautious...)
[Elebi begins to descend...]
Deep, Tranquil Voice: Ergh... This is unbelievable... I can't imagine how anyone would be able to do this to me... [Pacing back and forth.]
Very High Voice: [Somewhat nervous.]...At least you're not alone, right...?
Shadow: [Glares at the one who spoke... He sighs, and lowers his head... He seems to be an average Umbreon.] I suppose... And there is no point fretting over it... We will have to keep moving until we find the answers... [Turns away.] And I want answers...
[The other Pokemon is a small, rabbit-like one. Buneary.]
Cream: That big meanie... He came out of nowhere and just warped me away... You're right Shadow! I want answers too!!
Shadow: Good. Then can we keep movin--Hm!? [Looks up, watching Elebi land silently.] ...
Elebi: [Her wings stop fluttering as her feet touch gently to the ground.]
...
Shadow: This is a new face... And you would be...?
Elebi: My name is Elicia... I don't mean to trouble you...
Shadow: ...Hmph... Then if you would be so kind as to leave...
Cream: Shadow!! She might be able to help us!
Shadow: Oh? You really think so...?
...
Shadow: [Quietly... He scans Elebi.] Hmm... Maybe... Her presence is odd... [Outloud.] Alright... I apologize for that... My name is Shadow...
Cream: And I'm Cream! We're in a bit of a confusing problem...
Elebi: I can relate... I am an offworlder, so I have no clue what to do, but I am searching for those who can help...
Cream: You're not from here also? That's our problem!
Elebi: Hm? You're also from another world?
Shadow: Yes. We were transported here by a strange creature with many dark minions following behind... He had turned us into these creatures...
Elebi: (...If I were any bit of normal at the moment, I'd assume one of them was an Eclipse... But I'm not sensing anything from them specifically... I still wonder how this works...) I'm... I'm sorry to hear that... But if you need any help finding out some answers to the questions you have, I could probably support you.
Shadow: Then I have jumped to conclusions... Alright... We stand a better chance with three.
Cream: Thank you so much Elicia! We owe you!
Elebi: Aw, not at all! If we're all from other worlds, we should stick together.
Cream: So true!
Elebi: Well, we'd best keep moving... Don't worry about the dark, I've got that covered. (Carbuncle?)
Carbuncle: (I understand.)
[Carbuncle cojures the light around Elebi once again.]
Cream: Whoa! How did you do that?!
Elebi: [Giggles.] Just a little trick. C'mon, let's hurry!
Cream: Right! [Walks to Elebi.]
Shadow: [Staring off...] ...Hmhmm... Have you followed me, even here...?
Elebi: Shadow? 'You coming?
Shadow: [Closes his eyes...] ...Hm... [Opens his eyes and turns around, toward Elebi and Cream.] Yes... I was just puzzled by something...
[Shadow catches up. The three make way for the edge of Treeshroud Forest.]
...
...
...
Carbuncle: (Lord Hideaki...?)
Hideaki: (Yes, Carbuncle...? Is something troubling you...?)
Carbuncle: (Indeed... Did you happen to feel the abnormal disturbance in the Eclipses' order?)
Hideaki: (I did indeed feel disorder... A moment in time, the Eclipses trudged through Darkness... The source is still unknown... The gentle Light that seemed so unwavering has failed for the very first time... Though it has returned to them, it is a burden to bear in our thoughts that the Eclipses' chance of sinking lower into cruelty...)
Carbuncle: (Yes... It is... I will continue to play my part. If it happens again, then I will have to assume it has to do with... Him...)
Hideaki: (Pray tell what He is experiencing...)
Carbuncle: (My lord... that is not all... there is but another.)
Hideaki: (...You are correct... this other... his purpose is a terrifying one...)
--E N D I N G--
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Status:
If you've kept up thus far, you've probably a reader of my journal. If not, I commend you! ...Well, either way, I commend you. xD