Sapphire stared through the window as the submarine surfaced over the ocean, gasping at the sight. The sky was dark with clouds, rain pouring down upon them. Sapphire could hear each drop of rain hit the window with a loud thud, worry starting to build up at the thought of the window getting destroyed from it. "Oh my gosh…" Sapphire looked at Shelly, seeing the worry on her face. "It's awful out there…"

"I tried to warn you…"

"This… This is…" Sapphire looked at Archie as he approached the window, staring in disbelief. "I… I only wanted… I wanted to make... a world where Pokémon could live on… I-In peace…" Sapphire frowned, shaking her head as she placed a hand on his arm. "I tried to warn you. I tried to warn all of you. This is what Archibald tried to do years ago. Sir, I do hope you're happy. You've awoken Kyogre. Your job is complete."

"This isn't what any of us wanted, Sapphire. Please, we need to stop him." Shelly pleaded, watching Sapphire turn away. "I don't know if I can. I foresee many outcomes, most of which are not good. I doubt we can stop such a force. I only had a single mission in mind. Come here, check on the remaining gem inhabiting this Region, and go home. I know what became of one of those gems, but…" Sapphire looked down, removing the glove from her right hand. "I couldn't touch her. If I can't do that, how am I expected to stop her?"

Archie glanced at the Orb, brows furrowed as he placed a hand on Sapphire's shoulder. "Sapphire, I… Look, I'm sorry. Just… Please tell me you're not the same Sapphire from before. The one who ruined Hoenn and my ancestor's life." Sapphire sighed, shaking her head. "This is what I meant. I told you that I'm not and you didn't listen." Archie frowned, turning Sapphire to face him as he took her right hand. "I know what you told me, but I want your honest word. Look, I know I did an awful thing, but I'm going to fix my mistakes because staying mad at me won't do it. Just tell me the truth or else Arceus forbid that I poof you."

"Archie-"

"Don't try to defend for me, Shelly." Sapphire muttered, looking up at Archie as she brushed her bangs away. "I promise you that I am not the same Sapphire that ruined everything. That's my honest word." Archie grinned, patting Sapphire's shoulder as he chuckled. "Then allow me the honor of apologizing for my accusations." Sapphire nodded, looking down at her gem. "Let's find Kyogre before it gets worse."

"Sir!" Sapphire and Archie turned to attention to Shelly, staring as she pointed up. "Look!" The two craned their neck to look at the sky, watching the clouds clear up suddenly. "What's going on..?" The sun shone brightly, suddenly beating down upon the team as the grunts removed their bandannas to wipe sweat from their foreheads. "It's gotten so hot… What's going on?"

"Maxie.. He must've awoken Groudon some time ago. Meaning we've got less time than we think we do." Archie looked at Sapphire, holding the Orb close as he got on one knee to be at eye level with her. "We need to find out where they're heading. Any ideas, Sapphire?" Sapphire looked down, placing a hand under her chin and she frowned. "Well… If I remember correctly, Groudon and Kyogre were always at war with each other. If we find Kyogre, we'll find Groudon. I don't kno where we'd find them, though."

"I do." Archie stood up and called out to the grunts. "Set coordinates for Sootopolis City! Shelly, you and Sapphire will go ahead to meet us there!" Shelly nodded, grabbing a Pokéball from her belt. "Sootopolis City? Why there, sir?" Sapphire asked as she approached Shelly. "There's some things Archibald did after you left the Region, one of them was visiting the city to meet with a colleague, I believe. I'll explain more when we get there. Now, go."

"Yes, sir." Shelly said as she tossed the Pokéball, letting out a Pokémon similar to the one Matt had before Sapphire got in the submarine. "Let's hurry." Sapphire nodded as she climbed onto the Pokémon with Shelly, hanging on with both hands. "To Sootopolis City, Crobat!" The Crobat cried out, flapping its wings as it took to the skies. Sapphire looked up at Shelly as the Crobat glided across the sky, seeing the look of concern on her face. "You're worried."

"Archie worked so hard to get this far and I should've learned of everything sooner. I should've found out what was going on and stopped him." Shelly muttered, a slight shake in her voice. Sapphire placed a hand on her arm and shook her head. "It's not your fault. I should've warned him as well, but I didn't want to be caught. Steven and Connie would be ashamed of me if they knew what Ruby and I were doing."

"Stone?" Sapphire shook her head, looking down. "No. A different Steven. He… He's somebody I care about. Somebody back home waiting for me. I have to finish what I intended to do here before I can go back home." Shelly nodded, placing an arm around her as the Crobat started to go down. She smiled at her, crouching over the gem as rain started to pelt down upon them. "We'll get this over with and you'll be home to Steven in no time. I promise, Sapphire."

"Cro!" Sapphire looked down as Crobat dove towards a mountain with a large crater in it, a small town coming into view. Just nearby in a large pool of water was Kyogre, facing off what she assumed was Groudon. The Crobat swooped down, avoiding the two Legendaries as he landed nearby. Sapphire and Shelly hopped off, staring at the two beasts in concern as the sky cleared up. "We have to do something. We simply can't wait for Archie to arrive."

"There's nothing we really can do until he arrives. We have to wait." Sapphire frowned, closing her eye. The only thing she could see was darkness. Surely, it wouldn't come down to that, would it? She shook her head, trying to find a solution, but none came to her. "Shelly, there must be something we can do..!"

"There isn't.. We have to- Sapphire..?!" Shelly placed a hand on Sapphire's shoulders, staring with wide eyes as the gem shook. "We have to..! There must be something..! Because all I see is darkness..! If we wait, that's all we'll have..! Please, we must think of something..!" Shelly frowned, looking at her Crobat before pointing ahead at Kyogre. "Crobat, Poison Fang!" Crobat cried out and swooped ahead as Sapphire watched, shutting her eye as it got close. She saw the sky growing dark once again, but something red was falling from the sky. Something that cried out until she saw the red gem on its hand. "Ruby…"

"Where is your leader?" Sapphire opened her eye, looking up as a man with red hair walked up to them, holding a Pokéball in his hand. "Who are you?" Shelly stood behind Sapphire, holding her close as she glared. "Maxie. He's the Leader of Team Magma. Archie said you woke Groudon." Maxie nodded, sighing as he held a hand out. "Yes, but I see the error in it now. I'm here to stop it. My best grunts are coming with my Admins to stop him. Now, where is Archie?"

"Right here." Sapphire turned again, watching Archie approach with the grunts behind him. She was surprised she didn't hear the submarine surface. "You woke Kyogre, I see." Archie shook his head, sighing. "I didn't know he would do this. Listen, we need to set all differences aside. If we let them fight like this, they'll-" Maxie held up a hand, looking at Groudon. "I came here to propose that idea. Though, looking at it now, I don't know what to do."

"Surely, we have Pokémon that can defeat them. I just hope you didn't come alone, Maxie."

"I didn't, but I'm starting to wonder if sending her off on her on was a good idea." Sapphire's eye widen as she stepped forth. "You sent Ruby alone?! Why?! She could be lost or worse, she could be falling to her death right now!" Maxie held his hands up in defense, staring at Sapphire in surprise. "But she's a gem. She'll just reform, right?" Sapphire shook her head. "Not if she doesn't know where she'll land! Where is she now?!"

"Sir, up there! There's something falling!" Sapphire looked up as a grunt pointed, gasping as a Crobat was diving down after a Magma Grunt. It was Ruby! "RUBY!" Sapphire stepped forth, crouching down until Archie placed a hand on her shoulder. "What are you doing?" Sapphire looked up, keeping her eye on Ruby as she gritted her teeth. "I'm going to save her! I'm going to save my Ruby!" Sapphire jumped up, letting herself float up to Ruby as he called out again. "Ruby!" She held her arms out, fighting back tears until Ruby was close enough for her to wrap her arms around her. She looked down at Ruby, holding back sobs. "Sapphire?"

"You're ok! Ruby, you're ok!" Sapphire cried out as she held Ruby close, lowering herself to Sootopolis slowly. "Thank goodness you're ok!" Ruby held on as the two landed near the edge of water that surrounded the town, holding her close. "I saw you fall from the sky and I-I panicked..! I thought I was going to lose you!" Sapphire sobbed, clinging to Ruby as the two fell to their knees. "Sapphire, look at me. Don't cry. Please. I-I… I'm sorry, I couldn't stop Maxie. He… He wouldn't listen to me and… I couldn't grab the Orb." Sapphire sniffled, rubbing her face as she looked up at Ruby, shoving her bangs away.

"I couldn't stop Archie, either..! We came here as soon as possible when… When Maxie appeared and I thought the worst..! I thought he did something to you!" Ruby shook her head, wiping Sapphire's tears away as she kissed her forehead. "I'm here now. That's all that matters. I'm safe." Sapphire nodded, resting her head under Ruby's head as she tried to calm down. "We have to stop them."

"Ruby!"

"Sapphire!" The two turned as Archie and Maxie ran over, eyes wide as they skidded to a stop. "Sapphire, don't do that again..! You had us frightened..!" Sapphire looked at Archie, frowning as she shook her head. "I'm sorry, sir. I had to save her. I can't lose her. I can't lose Ruby. I-" Sapphire gasped as Ruby screamed, staring at the sky as rain pelted down. "There's no time. We have to stop Kyogre."

"Ruby." Ruby looked at Sapphire, taking her hands as they looked at one another. "We have to stop them. Together." Ruby nodded, looking her in the eye as she rested her forehead against Sapphire's. "We need Garnet." Sapphire nodded, wrapped her arms around Ruby. "Let's do this, then." Ruby picked up Sapphire and held her close, pulling her into a kiss as the two were enveloped in light, fusing them together. The two team leaders raised an arm to shield the light from their eyes, staring in surprise as a new person stood in place.

"Members of Team Aqua and Magma, Garnet is back in business!"