Here's mine:
Ruby/Sapphire Sequels:
> Deoxys has fallen from space, bringing meteors with it.
> The meteors have triggered a full scale eruption of Mt. Chimney.
> Lavaridge Town has been destroyed in the eruption.
> Meteors continue to fall across the land.
> Team Magma and Aqua reform, both hoping to catch Deoxys.
> Team Magma want to catch Deoxys and use it to continue to make the volcano erupt.
> Team Aqua want to kill Deoxys to stop it filling the waters with space rocks.
> Obviously you don't want to either harm Deoxys or drain the world of water, so you are opposed to both.
> New evos of old pokemon are in the Hoenn pokedex. We get Gallade, Probopass, Magnezone, Budew/Roserade, Chingling, Dusknoir, Leafeon, Glaceon and Froslass.
> HMs are Surf, Fly, Rock Climb, Dive and Waterfall.
> You start journey in Oldale Town, get your starter from Prof. Birch, start your journey.
> Hear about meteors as you travel, see them on your journey.
> Brendan/May work at the Space Institute, and set out to find Deoxys too to learn about its origins. You meet them as you travel, and they dish out advice and stuff.
> Norman is still the Normal-type Gym Leader, but the Gym is revamped and he's your first Gym battle. Probably has a Slakoth and Zigzagoon.
> You first meet the bad guys in the Devon Corporation in Rustboro City. Magma want to steal strong Poke Balls to help capture Deoxys. In the other game, Aqua want to steal attack-boosting items to strengthen their pokemon in order to eliminate Deoxys. You stop them of course, and get the PokeNav as thanks.
> Roxanne is the second Gym leader, and she now has stronger pokemon. She owns a Probopass and there are references to a newly discovered cave where she evolved her Nosepass recently. Located on the westernmost coast of the Dewford Town island with Rock Climb (now a HM). Petalburg Woods has an extra area with a Moss Rock now, and Shoal Cave has an Ice Rock. Convenient, huh?
> Mr.Briney left home to become a sea captain, so we have to press on through Rusturf Tunnel to get to Verdanturf Town. This is when we start to hear about the eruption and the people displaced by the volcano activity. A family in one house talks about their nephew's improved health and his bid to become a better trainer.
> There's a mini-fight at the Daycare Centre, where a Team Magma/Aqua member is trying to steal pokemon to help capture/kill Deoxys. You kick ass, the daycare couple let you stash your pokemon there in future, maybe even reward you with an Egg.
> We get to Mauville City. Many Lavaridge refugees are here now. Apparently, the eruption has cut off access to the north of Mauville. Large mountainous deposits now block the way. They'll be Rock Climbable later, however. You may find some different pokemon in the grass around here like Spoink, which have fled the lava floes.
> Wattson has retired, and the Gym here has been closed. A new Battle Frontier is under construction southeast of Mauville City.
> You are told about a new Gym in Slateport City, so you head to there. Here, along the beach, a retired shipbuilder from Stern's Shipyard has set up a Ground-type Gym. We're talking Vibrava, Claydol, Sandslash, Barboach.
> When you win, the Gym Leader gives you a free ride to Dewford City like Mr.Briney used to. Dewford Town is the same, but the eastern side of the island is accessible with Rock Climb when you get it. It'll contain a 'Mt. Coronet' style place to evolve your Nosepass or Magneton. Now the fourth Gym (without any leeway to bypass the Gym), Brawly's Fighting-type pokemon are much tougher. Breloom, Hariyama, Machoke. Once you win, you get HM Surf, so you can explore the water routes north and east of Dewford.
> So, now what? We press on towards the Weather Institute. We'll meet Brendan/May, who'll explain about Deoxys. Suddenly, shit is going down at Lilycove and he/she Flys off towards there. Winona's gone from Fortree City too! We travel there and discover Team Magma and Aqua battling Deoxys. It defeats their pokemon and flees. Brendan/May and Winona watch on in awe at its power, Winona Flys home and is then battleable. Rocks are strewn across the bay so you have no choice but to return the way you came. Winona has Altaria, Skarmory, Crobat, Swellow. You get HM Fly when you win.
> Mt.Pyre is fairly uneventful.
> With Winona defeated, Lilycove Bay is open to Surf on, and you get to Mossdeep City. Of course, the bad guys are attacking the Space Centre to find more info about Deoxys. After some battling, Brendan/May team up with you to finish off the leaders' assault. They flee empty-handed. Apparently, he/she's had a tip-off that Deoxys is hiding in Meteor Falls. But how to get there? You'll need to defeat Tate and Liza to use the HM Rock Climb, which Brendan/May give to you. Tate and Liza have Solrock, Lunatone, Grumpig, Gardevoir... and similar pokemon. Double battle as usual.
> With Rock Climb, you can now access the area north of Mauville. Lavaridge is destroyed, so you'll be taking a circular trip through the desert, around the volcano and west to Fallarbor Town. It has just escaped the fiery spews of the volcano, but the area is smoky and ashy and alive with lava and flames.
> Flannery has set up base here, so you'll be battling her seriously stronger Fire-type team. Magcargo, Torkoal, Camerupt, Ninetales... it's a lot tougher than a few years ago! You'll have access to HM Dive now.
> With Flannery defeated, the final showdown begins. You head to Meteor Falls (the plot forces you to) where you'll find your version's enemy grunts (Magma or Aqua) and defeat them all. You'll come out on the mountainside and Rock Climb to the top of the mountain, where you'll fight off the Team leader for the right to battle Deoxys. They are defeated and disband in disgust. You fight Deoxys and the meteors stop, and the volcano calms down.
> You can now move on with your quest to become a champion. Pacifidlog Town is the same as before, and Dive allows you to explore more areas and reach Sootopolis City, where Juan will have more-or-less the same team as before. He mentions that his old mentor Wallace was defeated and is no longer the Champion.
> You reach Ever Grande City, and Sidney, Phoebe, Glacia and Drake remain intact. You open the doors to the Chmapion... Wally! He finally made it. He has Gardevoir, Altaria, Magnezone, Roserade and Delcatty. He's strong! But you defeat him anyway.
> The Battle Frontier is now open for business.
> Steven is found in Meteor Falls examining meteors and has his tough Emerald team to battle.
> You get a call from the Gym Leader in Slateport after your win. His old boss (Captain Stern) has discovered an extremely fast underwater current that goes to a string of small islands (the ones south of Pacifidlog Town on the map) quickly and safely. You hop in Stern's submarine and go there with him.
> A new mini-plot develops. The island chain is experiencing heavy rain/intense heat, and some think that Kyogre/Groudon is to blame. Some remaining Team Aqua/Magma members investigate this claim as well.
> The islands host many new locations. One 'island' is an oil-drilling operation, another a large uninhabited jungle area (with Jirachi discoverable at its heart), another area has Dive-able underwater city ruins. Other islands have regular towns with mini-stories like the Sevii Islands.
> Wallace has retired to a small fishing village and is battleable there with a team similar to his Champion team.
> The plot takes you across islands with high-level pokemon, culminating in the discovery that Kyogre or Groudon (depending on your version) have been awoken because of an oil drilling operation in the sea. You fight Magma/Aqua off and quell the legendary beast, thus ending the game.
Ruby/Sapphire Sequels:
> Deoxys has fallen from space, bringing meteors with it.
> The meteors have triggered a full scale eruption of Mt. Chimney.
> Lavaridge Town has been destroyed in the eruption.
> Meteors continue to fall across the land.
> Team Magma and Aqua reform, both hoping to catch Deoxys.
> Team Magma want to catch Deoxys and use it to continue to make the volcano erupt.
> Team Aqua want to kill Deoxys to stop it filling the waters with space rocks.
> Obviously you don't want to either harm Deoxys or drain the world of water, so you are opposed to both.
> New evos of old pokemon are in the Hoenn pokedex. We get Gallade, Probopass, Magnezone, Budew/Roserade, Chingling, Dusknoir, Leafeon, Glaceon and Froslass.
> HMs are Surf, Fly, Rock Climb, Dive and Waterfall.
> You start journey in Oldale Town, get your starter from Prof. Birch, start your journey.
> Hear about meteors as you travel, see them on your journey.
> Brendan/May work at the Space Institute, and set out to find Deoxys too to learn about its origins. You meet them as you travel, and they dish out advice and stuff.
> Norman is still the Normal-type Gym Leader, but the Gym is revamped and he's your first Gym battle. Probably has a Slakoth and Zigzagoon.
> You first meet the bad guys in the Devon Corporation in Rustboro City. Magma want to steal strong Poke Balls to help capture Deoxys. In the other game, Aqua want to steal attack-boosting items to strengthen their pokemon in order to eliminate Deoxys. You stop them of course, and get the PokeNav as thanks.
> Roxanne is the second Gym leader, and she now has stronger pokemon. She owns a Probopass and there are references to a newly discovered cave where she evolved her Nosepass recently. Located on the westernmost coast of the Dewford Town island with Rock Climb (now a HM). Petalburg Woods has an extra area with a Moss Rock now, and Shoal Cave has an Ice Rock. Convenient, huh?
> Mr.Briney left home to become a sea captain, so we have to press on through Rusturf Tunnel to get to Verdanturf Town. This is when we start to hear about the eruption and the people displaced by the volcano activity. A family in one house talks about their nephew's improved health and his bid to become a better trainer.
> There's a mini-fight at the Daycare Centre, where a Team Magma/Aqua member is trying to steal pokemon to help capture/kill Deoxys. You kick ass, the daycare couple let you stash your pokemon there in future, maybe even reward you with an Egg.
> We get to Mauville City. Many Lavaridge refugees are here now. Apparently, the eruption has cut off access to the north of Mauville. Large mountainous deposits now block the way. They'll be Rock Climbable later, however. You may find some different pokemon in the grass around here like Spoink, which have fled the lava floes.
> Wattson has retired, and the Gym here has been closed. A new Battle Frontier is under construction southeast of Mauville City.
> You are told about a new Gym in Slateport City, so you head to there. Here, along the beach, a retired shipbuilder from Stern's Shipyard has set up a Ground-type Gym. We're talking Vibrava, Claydol, Sandslash, Barboach.
> When you win, the Gym Leader gives you a free ride to Dewford City like Mr.Briney used to. Dewford Town is the same, but the eastern side of the island is accessible with Rock Climb when you get it. It'll contain a 'Mt. Coronet' style place to evolve your Nosepass or Magneton. Now the fourth Gym (without any leeway to bypass the Gym), Brawly's Fighting-type pokemon are much tougher. Breloom, Hariyama, Machoke. Once you win, you get HM Surf, so you can explore the water routes north and east of Dewford.
> So, now what? We press on towards the Weather Institute. We'll meet Brendan/May, who'll explain about Deoxys. Suddenly, shit is going down at Lilycove and he/she Flys off towards there. Winona's gone from Fortree City too! We travel there and discover Team Magma and Aqua battling Deoxys. It defeats their pokemon and flees. Brendan/May and Winona watch on in awe at its power, Winona Flys home and is then battleable. Rocks are strewn across the bay so you have no choice but to return the way you came. Winona has Altaria, Skarmory, Crobat, Swellow. You get HM Fly when you win.
> Mt.Pyre is fairly uneventful.
> With Winona defeated, Lilycove Bay is open to Surf on, and you get to Mossdeep City. Of course, the bad guys are attacking the Space Centre to find more info about Deoxys. After some battling, Brendan/May team up with you to finish off the leaders' assault. They flee empty-handed. Apparently, he/she's had a tip-off that Deoxys is hiding in Meteor Falls. But how to get there? You'll need to defeat Tate and Liza to use the HM Rock Climb, which Brendan/May give to you. Tate and Liza have Solrock, Lunatone, Grumpig, Gardevoir... and similar pokemon. Double battle as usual.
> With Rock Climb, you can now access the area north of Mauville. Lavaridge is destroyed, so you'll be taking a circular trip through the desert, around the volcano and west to Fallarbor Town. It has just escaped the fiery spews of the volcano, but the area is smoky and ashy and alive with lava and flames.
> Flannery has set up base here, so you'll be battling her seriously stronger Fire-type team. Magcargo, Torkoal, Camerupt, Ninetales... it's a lot tougher than a few years ago! You'll have access to HM Dive now.
> With Flannery defeated, the final showdown begins. You head to Meteor Falls (the plot forces you to) where you'll find your version's enemy grunts (Magma or Aqua) and defeat them all. You'll come out on the mountainside and Rock Climb to the top of the mountain, where you'll fight off the Team leader for the right to battle Deoxys. They are defeated and disband in disgust. You fight Deoxys and the meteors stop, and the volcano calms down.
> You can now move on with your quest to become a champion. Pacifidlog Town is the same as before, and Dive allows you to explore more areas and reach Sootopolis City, where Juan will have more-or-less the same team as before. He mentions that his old mentor Wallace was defeated and is no longer the Champion.
> You reach Ever Grande City, and Sidney, Phoebe, Glacia and Drake remain intact. You open the doors to the Chmapion... Wally! He finally made it. He has Gardevoir, Altaria, Magnezone, Roserade and Delcatty. He's strong! But you defeat him anyway.
> The Battle Frontier is now open for business.
> Steven is found in Meteor Falls examining meteors and has his tough Emerald team to battle.
> You get a call from the Gym Leader in Slateport after your win. His old boss (Captain Stern) has discovered an extremely fast underwater current that goes to a string of small islands (the ones south of Pacifidlog Town on the map) quickly and safely. You hop in Stern's submarine and go there with him.
> A new mini-plot develops. The island chain is experiencing heavy rain/intense heat, and some think that Kyogre/Groudon is to blame. Some remaining Team Aqua/Magma members investigate this claim as well.
> The islands host many new locations. One 'island' is an oil-drilling operation, another a large uninhabited jungle area (with Jirachi discoverable at its heart), another area has Dive-able underwater city ruins. Other islands have regular towns with mini-stories like the Sevii Islands.
> Wallace has retired to a small fishing village and is battleable there with a team similar to his Champion team.
> The plot takes you across islands with high-level pokemon, culminating in the discovery that Kyogre or Groudon (depending on your version) have been awoken because of an oil drilling operation in the sea. You fight Magma/Aqua off and quell the legendary beast, thus ending the game.