His journey back to Sinnoh is arduous and rough, but at last, he finally returns. Being quite shocked by how much it has changed in nearly a hundred years, he asks around to find Leigh, and after some difficulty, he at last finds her house...

*Knock* *Knock*

A kind-eyed elderly lady opens the door.
"May I help you?" She answers, with some effort, it seems it took a lot for her to answer the door.

"L-Leigh?" Spira is practically tearing up. "Is it really you?"

"Who are you?"

"I guess you don't remember me, I'm sorry to have bothered you, ma'am."

...

Despondant, Spira leaves, to Mt. Coronet and there meets Dialga, by pure chance.

SPIRA KAND, CURSED SPAWN OF DARKRAI, WHY HAVE YOU COME? Dialga booms telepathically to Spira. (Considering Dialga having done something similar to Adaman, I figured this would be fine)

"I just want to be in my own time. I am willing to do what it takes."

GIVE UP YOUR BIRTHRIGHT, AND IT SHALL BE DONE!

He nods.

A brilliant flash of light from his arm, and the Mark of Darkrai fades from it, as time reverses solely for Spira...

Back in a more familiar time, Spira rushes to the hospital in which Leigh had been comatose...

*Gasp* *Pant* "Leigh! I need to see Leigh!" He manages to get out to a nurse.

"Oh, Spira! Perfect timing, it seems that she has woken!"

As the nurse leads Spira to Leigh's room, he is sweating from nervousness.

"Here we are." The nurse smiles and winks as she returns to her duty.

"S-Spira..." Leigh starts, smiling, "I guess I overdid it huh?"

Spira sobs, in happiness.

*SOME TIME LATER*

A young man, in his late twenties finally finishes the boat ride to Creshire, on a mission. After seeking out one of the people that matches the description he was told by his parents, and their parents, he addresses her.

"Ms. Shiva?"

"You don't know me, but you did know my grandfather. This is something that he wanted done, but wasn't able to do himself because of health.  I trust that you can  handle the rest."

The young man, who still hasn't identified himself, hands Shiva a yellowed letter, and leaves...

~Thus Ends the story of Spira, the breeder out of time~

managed to work things out and getting a happy ending, and being reunited with and even married to Leigh!

That's...not that easy to answer as there are many Pokemon Shiva has captured and/or befriended over the course of the story that are still close to my heart and would consider personal faves, independent of how often they were in her party or how often/not often they got to battle. On the highest spot of the ladder are definitely Primal Eevee, Delphox and Azumarill though:

Primal Eevee (being a Primal Espeon currently after having evolved into Primal Glaceon, with plans of the final evolution being a Primal Jolteon) has a plain awesome diversity and potential within itself, being able to evolve three times and therefor making it possible to build up a movepool that'd be unique af and suprise a foe with ease. Trainer tries to counter my Primal Eeveelution with a Pokemon of a Type that's SE against it? Watch me having an ace up my sleeve by displaying a move that for example Espeon could never have, like Ice Shard and Icy Wind from the time it were a Primal Glaceon. Plus playing with such a Pokemon is simply enjoyable due to my personal fondness of Eeevee and Eeveelutions.
Delphox...was a wishlist 'Mon, everything about that furry mage matched Shiva, basically screaming for her training one of these foxes. I'm glad that this wish got fulfilled relatiely early and in a cool way even if thinking back to how Shiva has encountered Fennekin, the evolution process was fun to follow, and I always enjoyed interacting and battling with him; not only did it became of of Shiva's strongest Pokemon eventually but also one that fits her interests and personality all too well. Awesome synergy alongside Nightshade (Cherrim) too, due to Sunny Day + Delphox's Fire typ'd moves being boosted + Cherrim's Flowe Gift ability!~
Azu is another Pokemon that joined Shiva pretty early, and over the course of the game became the powerhouse! Starting out as a tiny and meek mouse that hid away in a top hat (or Shiva's sleeve) it became a brave and confident Azumarill in the long run, which is...similar how Shiva herself grew slowly but steady. It was far from an easy journey for both but they made it together eventually, especially since Azurill started out with -1(!)Happiness and ended up with full 5 Happiness and Loyality.

I've kept track of who caught what Pokemon in a seperate tab in my charasheet, both because I enjoy documenting things like that and because it was convenient for potential trades + planning out our party of six Pokemon together in MetaThread before important trips where a PC would be unaccessible. No particlar order:

-Heart: That's a tie between Axew --> Fraxure --> Haxorus (Koa) for how that Pokemon really fits Heart me feels + the rivalry between that dragon and Shiva's Cottonee --> Whimsicott was fun to roleplay as well as that Electric/Poison type'd Pikachu (Inthra) he caught in the Safari Zone. Sad that this one didn't get that much of the spotlight.

-Nathan: Hands down, it's Calam (Absol). Really enjoyed how that Pokemon was introduced early, followed us around all silently and had their purpose/intentions releaveled muchhhh later, that's something I really like in roleplays. Bonus: While I really disliked all the in-chara drama that Delta Houndour (Orthros) from the scary dreamworld brought the Ventus and Shiva and how the encounter with the Houndours there traumatized these two, I outta-chara liked how Nathan was non-condemning towards that doggo and treated him like any other Pokemon.

-Ventus: Ekans --> Arbok (Aspis), that poisonous snake that matched Ven's person sooo well, slightly more than Togekiss (Raphael) even which is a very very close second favorite. Battlewise Aspis was amazing with her elemental bites attacks, she helped us as a party out of complex situations more than once, and I really really liked how Ventus managed to bond with such a at first glance 'dangerous' Pokemon and how protective she eventually became towards him.

-Terra: That's an easy one, it's Flygon (Genie) that fairy-like desert dragon with her mind focused on mischief. I loved that scene where Shiva and Genie played hide-and-seek and how she managed to have a ride on Genie's back much to Terra's suprise, given Genie - if I remember that correctly - lets not even Terra on her back.

-Spira: Dusknoire (Toya). Might be that I'm biased due to loving Dusknoire's character in the Explorers of Time/Darkness/Sky, but something about that ghost by Spira's side makes me really like him. His protective Bannette Noire is a close second.

Dies Irae, Larry, Nylon and Sage were too little involved with their Pokemon for me to properly decide on a favorite 'Mon of theirs, sorry about that!

For that question I will consider solely encounters I took, for the sole reason that these are the ones I at least remember properly, my memory on what encounters everyone else took is too foggy already, sorry again!

Either way, it's that strange genetically-drifted Poochyena with tiny tiny bioluminescent Butterfree-wings on his back that Shiva met on Route 4, which eventually became her strong, loyal and special butterwolfly. Loved how over the course of the story Shiva managed to learn more about how hat Poochyena was a uique phenotype and how it played into her interest and upcoming career in Pokemon Breeding.
A close second is that Espurr from the same dreamworld these Delta Houndours roamed, enjoyed how she met that once and convinced him to come along with her (which was, by solely appearing protective when Espurr was chased by one of the deltadogs and a lucky roll caused Espurr to jump into her opened arms).

That's a question I can answer relatively easy, as for me it's that huge Arcanine we met down the Crater of Myth, that one that took care of Eggs from - in our time - endangered species of Pokemon. That one that made us pledge when we took some of the Eggs with us (I remember me having gotten the Egg of Minicorn + Flabebe, nathan the one of Dratini and the Megastone for Absol and Heart the Egg of Moltres) in the hope of working on a slow but stead repopulation of the Pokemon in question. Such a graceful and majestic Pokemon with a purpose that I found the most interesting and meaningful, the scene with that Arcanine were to me emotional (in a positive way) and not easy to play, yet I loved it to bits.

Easily Calam.  He was quite possibly the most important of our regular pokemon in terms of the overall plot thanks to several different traits and circumstances, and it was all brilliantly implemented.

Honorable mention to Princess and Zippy, showing that even small bugs can aspire to achieving big things, becoming respectable rulers in their own right by the end of the campaign.  This is our land, Deoxys, not yours!

Shiva: This is a tough one, but if I had to pick one, I'd probably say it's Azu.  Seeing them go from a depressed Azurill to a confident and strong Azumarill was easily a highlight.

Terra/Ventus: As loathe as I am to admit it, Aspis was probably my favorite of Windos's mons over the course of the campaign.  I'm still not really a fan of how they technically displaced Raphael as Ventus's primary pokemon, but seeing Aspis begin to mellow out a little was good development.  I still kinda wish that Ventus could have stuck around and he and his pokemon could have seen more meaningful development, because there was a lot of potential there.

Heart: definitely Koa, the little dragon that could.  Not much more to say here.

Spira: honestly, I don't remember Spira's party all that well, but I do remember one moment in particular that stood out: how Spira's Magcargo evolved from Slugma.  Pokerole 1.0's evolution requirements were wild.  A little too wild, even.

Valder: absolutely his Keenglaive.  While we never did get to see what it could do because Pawniard evolved right before Valder vanished, the species is an important part of Creshire's history, and actually learning about it was really cool.

I think my favorite encounter was the Safari Cup (slightly cheating cuz it was a series of encounters, but eh).  It gave us a good look at how competent trainers get scoped out by the League and its gym leaders, a look into the more conservationist side of the plot and region, and I even got a few rare mons out of it to boot.

I'm still slightly upset I didn't reach the finals though.  We never got to see that one trainer who was making waves competitively because we never reached the finals in any tournament.

Oh boy, there's a lot to list here as options.  Deoxys and Celebi, Seikamater, Landorus, Mesprit, Arcanine and Moltres, the Southern Wind, Aegislash, Latias and Latios, Genesect, Lurantis and Kingdra...

But I think Kazesidhe easily takes the cake.  While he wasn't particularly plot relevant, the fact that we kept running into Sid as we went further west and he always had something weird going on with his techniques was intriguing enough by itself.  Finding out that he was a modern incarnation of an old, completely custom member of the Legendary Beasts known as the East Wind though?  Mind blowing.