Melody rolled over a bit in her simple straw bed, looking around the crew room that she and her partner stayed in. She glanced at the Cyndaquil quietly sleeping in the room's other bed. Flynn seemed to have fallen asleep pretty quickly. Melody was tired as well, but all the thoughts rolling around her head made it hard to sleep.
(It's still hard to believe he's really back,) the Skitty thought. (I... I was sure I'd never get to see him again after what happened at Temporal Tower, but... there he is, alive and well.)
It had been nearly four months since the duo had stopped Temporal Tower's collapse and prevented the planet's paralysis. They had changed the future... but since Flynn was from a future that would no longer come to pass, he had vanished from existence as a result. Melody didn't even know it was going to happen until it had already started. In the moment, she tried to tell him how much he really meant to her, but... the words just wouldn't come out.
The months since then had been rough. (When I first returned to Treasure Town, I was... barely holding myself together,) she thought bluntly. She told everyone what had happened, and every time she had to tell the story, she struggled to recount Flynn's disappearance without breaking down. Over time, she'd slowly managed to make progress, getting back into her usual routine and trying to move on. Flynn had wanted her to go on living, and she had tried her best, but... she had missed him so much...
They had been a team for months, working together every day, protecting each-other and keeping each-other company. Flynn had helped her to be brave, and encouraged her to keep going when everything seemed hopeless. They had literally saved the world together. Suddenly losing Flynn after all that... Melody had felt like a piece of her was missing.
Then, just a few hours ago, Melody had been at the beach on the outskirts of town, tearfully thinking about all their time together. Bidoof had found her after a while, and he tried to comfort her, but it only helped a little. Partly because it was yet another thing that reminded her of Flynn.
After a minute or two like that, Bidoof cried out in shock, pointing a paw at a spot farther down the beach. Melody slowly got to her feet, turning to look at whatever it was. There was a bright, glowing light coming from... something, but the light was blinding enough that she couldn't see exactly what it was. After a few moments, the light faded away... and in its place, glancing around in confusion, was Flynn. When he noticed the Skitty, his confusion faded and he silently gave her a warm smile.
Melody stood there in shock for a few seconds, unable to process what she was seeing. Her legs were shaky as she walked up and reached out a paw to the Cyndaquil, desperately hoping he wasn't just a dream or a hallucination. Flynn rested a paw on her back, and she broke down again, crying tears of joy into Flynn's side.
Neither of them was really certain how he had returned exactly. Flynn said he'd heard Dialga's voice just as he regained consciousness, but he couldn't make out what exactly Dialga had said. Their best guess was that Dialga had revived Flynn because of everything he and Melody had done to prevent Temporal Tower's collapse. But if Flynn was truly alive again, that was enough for Melody; she didn't need to know exactly how and why.
(We can go back to how things were. We can continue our guild training together, exploring dungeons, helping other Pokemon... I-I have my best friend back.) The Skitty let out a wistful sigh. (But... in my heart, I'd still like us to be... more than that. I have no idea if he feels the same way, though.)
She had wanted to maybe tell him how she felt after they'd saved Temporal Tower and things had calmed down again, but... that hadn't worked out, obviously. Now she had another chance, but... (Should I risk it? What if he doesn't feel the same way? Especially considering he used to be human... What if I just make everything awkward between us? Is it worth the risk?)
Melody's train of thought was interrupted a little as she had to stifle a yawn. She was abruptly reminded just how late it was, and how tired she felt after everything that had happened that day. (I really should try and get some sleep,) she thought, settling back down onto her bed and trying to get comfortable. (Someday... I do want to tell Flynn how much he really means to me. But for the moment, at least... I'm just happy to have our friendship back...)
"Up and AT 'EM! It's MORNING!"
"Ugh..."
The morning after Flynn's return, he awoke to the sound of Loudred's usual wake-up call, followed by a tired groan from his partner. Letting out a quiet yawn, Flynn slowly got up, rubbing the sleep out of his eyes before glancing around. Team Sunrise's room was pretty much the same as he remembered, despite the time that had apparently passed since he disappeared. A warm smile formed on his face as his gaze turned to Melody, who was slowly getting out of bed as well. Flynn greeted his tired partner. "Good morning."
The Skitty jolted in surprise briefly when she heard Flynn, before remembering what had happened the night before. She turned to him and returned his smile. "Morning, Flynn." After a moment of hesitation, she walked up and nuzzled his side. "I-I'm really glad you're back. I really missed you."
Flynn happily returned the nuzzle. It had taken the former human a while to get used to that, but like with many other things since becoming a pokemon, he'd adapted eventually. "I missed you too."
They stayed like that for a few seconds, before Melody quietly said, "We, uh... We should probably get going, or else we'll be late for the morning briefing." She pulled away, walking over to the team's treasure bag and settling it on her back. Flynn thought he noticed a slight blush on her cheeks, but it might have just been his imagination.
Later that day, the duo made their way to Amp Plains. They'd picked out a rescue request from an Eevee, who had ventured into the dungeon hoping to find a thunder stone and had fainted. Thankfully, the Electrike tribe shouldn't be around this time of year, so the area shouldn't be too dangerous, but the team remained cautious nonetheless.
As was usual for Team Sunrise, Flynn led the way, keeping an eye out for wild pokemon and traps and picking which directions to go. Melody followed close behind, carrying the treasure bag on her back. She quietly hummed a tune to herself as she walked, but she stayed alert in case any wild pokemon tried to sneak up from behind. In general, though, they were able to handle the opponents around here without much trouble. Most foes fainted easily to a Flamethrower or Flame Wheel from Flynn, or a Double Slap or Feint Attack from Melody. Even if two or three wilds appeared together, Melody could Sing one to sleep to help even the odds.
Still, Melody was a little nervous. Partly because of the memories of the close call they'd had the first time they came here, and partly because of the general atmosphere of the area. The air was charged with electricity, and dark storm clouds loomed overhead. It probably seemed like a pretty nice place to be, if you're an electric-type, but Melody couldn't help but be a little on-edge.
(At least I have Flynn with me,) she thought. Having him by her side always made her feel stronger and braver. While he was gone, she'd had to team up with the other apprentices in the guild, and while they were all good friends and helpful teammates, it just wasn't the same.
After several floors, they stopped to rest near the stairs for a few moments before continuing. Flynn grabbed a couple apples out of the treasure bag and gave one to Melody. She decided to break the silence just as they finished eating, asking a question she'd been holding onto for quite a while. "How long did you know... that you were going to disappear?"
Flynn flinched, and he averted his gaze to stare at the floor. "...Dusknoir told me, when you left to activate the stoneship."
Melody sighed. "...I want to say you should have told me then. But at the same time... if you had, I'm not sure I would have had the resolve to do what we needed to do. So maybe it's for the best that you didn't."
"...Still, I'm sorry."
Shaking her head, Melody moved a little closer to Flynn. "Just... please don't hide something like that from me again."
Flynn nodded. "I promise."
"And... I know you can't promise that nothing will ever happen to you, but... please, try not to leave again."
"I wouldn't dream of it," he replied, smiling warmly at her. Melody smiled back, and they remained like that for a few moments, gazes locked. Melody opened her mouth to say something, but ultimately stayed silent.
The duo were so distracted that they failed to notice a wild Mareep approaching until it launched a Thunder Wave at Flynn, paralyzing him. Melody recoiled in surprise, but quickly focused, turning to the Mareep. She dodged out of the way of a Thundershock, before retaliating with a Thunderbolt of her own, which dealt full damage thanks to Melody's Normalize ability. The Mareep collapsed, and after she was sure it had fainted, Melody returned her attention to Flynn.
The Cyndaquil grimaced, struggling to move his muscles. This was far from the first time he'd been inflicted with paralysis like this, and he knew the effects would wear off in a few minutes. In the meantime, he'd just have to deal with it, unless they had a cheri berry or a spare heal seed. But Melody had her own suggestion. "I can cure it. Just give me a moment."
Flynn wasn't sure what she had in mind, but he managed to give a small nod with a bit of effort. After a moment, Melody started to sing. It sounded different from when she used Sing to put enemies to sleep, or the rare occasions he heard her sing normally. This tune had a soothing, almost bell like quality to it. It was nice.
(But then again, Melody's singing always sounds nice,) Flynn thought.
Strangely, his paralysis started clearing up. Soon, he found he could move normally again, just as Melody finished. He tilted his head, and she answered his silent question. "That was Heal Bell. I learned it a few weeks ago. It only heals status ailments, not actual damage, but it's handy for conserving supplies."
Flynn nodded, and the two of them got ready to continue up the stairs. They'd lingered a little too long on this floor, and the wind was beginning to pick up, which was a sign they needed to move on before that floor of the dungeon shifted.
The rest of the mission went pretty smoothly. They found the client a couple floors later, curled up in the corner of a room. He panicked briefly when Melody called out to him, but quickly calmed down when he saw their badges and treasure bag. "Whew! You two must be here to rescue me?"
"That's right," Melody replied. Flynn let her do the talking, as usual.
"Awesome! Thanks, uh..." The Eevee trailed off, not recognizing the explorer's species.
"I'm Skitty, and my partner here is Cyndaquil." Melody refrained from giving him their personal names, since he was only a client. She and Flynn were more open with their names than most pokemon, but still.
Eevee thanked the duo again, and Flynn used his badge to warp the three of them out. They still had to walk the rest of the way back to Treasure Town, but the Eevee was just glad to be out of that dungeon, so he didn't mind.
Author's Note: This is my first real attempt at actually writing anything like this, and I'm sure it's not really all that good. But I'm reasonably happy with how this is turning out so far. Though it's taken a lot of adjustments, polishing, and refining to even get it to this point. I've got the first three chapters already basically finished as of posting this, but I plan to space out posting them a little, to give some time to make any final adjustments and try to finish more chapters by then.
This is... probably slight AU, technically? After the first couple chapters like this, focusing on the time skip after the ending, I plan to cover the post-game story as well. But with my own slight spin on it. I've had bits of ideas and headcanon for a story like this building up for quite some time, but not enough to really make an adaptation of the full game.
If you have any comments or constructive criticism, please leave a review. I'm not sure how likely it is that I'll write any more stories after this, but I may as well try to make this one as good as I can.