A new aspect of these games is the special Delta Episode. This part of the game tells of a story of an asteroid coming towards the planet with ties to things that happened 3000 years ago. It is said to tie together the mysteries of Mega Evolution and gives the history of Hoenn. This is done with the help of characters such as Steven and Wallace. This page contains major spoilers so don't read it unless you want to be spoiled.

This story activates after you first beat the Elite Four. When you start your save it goes to Mossdeep City where Professor Cozmo is alerted to a disaster. A meteoroid is heading towards the planet, aiming for an island by Route 131. A Magma/Aqua grunt takes off her uniform and dons her normal clothing, proving herself to be Zinnia. She mentions things have got tricky because you stopped the primal Pokémon being revived

The game then starts in your house where Norman gives you a Pair of Tickets to the Mossdeep Star Show, suggesting you take your rival with you.

When you get to Petalburg, you will find Courtney/Matt with Wally. They will want his Key Stone and then your Keystone and will challenge you. Defeat them and they will mention going to Meteor Falls for the Leader's Key Stone. Wally thanks you but notes that his Key Stone is gone as it is. You then get a call on your PokéNav from Steven who asks you to meet him in Rustboro.

Magma Admin Courtney	Camerupt
Items	Level 53
	Magma Armor Solid Rock
	Attacks: Rock Slide Yawn Earthquake Eruption
	Hold Item: No Item

Aqua Admin Matt	Sharpedo
Items	Level 53
	Rough Skin
	Attacks: Aqua Jet Taunt Agility Skull Bash
	Hold Item: No Item

Went to Rustboro and Steven was there with bad news that needs to be discussed. He tells the story of how 3000 years ago, talking about the war in Kalos that was stopped by a weapon made by AZ. Mr. Stone's Grandfather, using the story, created Infinity Energy using similar energy to the ones that weapon used.

He says that a huge asteroid, six miles in diameter, is on track to hit the planet, and Devon Corp is working with the Mossdeep Space Center to develop countermeasures but they need the Meteorite Shard for it and they are found in Granite Cave

When you get to Granite Cave, you meet Zinnia who is looking at the cave painting showing Primal Reversion and Mega Evolution and saying how ancestors passed down knowledge to her on how to Protect the World. Zinnia asks why you're there and then battles you. If you win, she'll give you a Meteorite Shard. After you get it, the Meteorite you got from Mt. Chimney glows again and she suggests you keep it with you. The Meteorite's image has actually changed in the bag. Steven will call and recommend you go to Mossdeep City

Pokémon Trainer Zinnia	Tyrantrum	Altaria	Salamence
Items	Level 55	Level 55	Level 57
	Strong Jaw	Natural Cure	Intimidate
	Attacks: Dragon Claw Crunch Earthquake Stone Edge	Attacks: Dragon Pulse Moonblast Flamethrower Hyper Voice	Attacks: Dragon Claw Crunch Fire Fang Thunder Fang
	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item

When you get to Mossdeep City, you will hand the Meteorite Shard over to Professor Cozmo as he explains the current plan. They intend to use the energy from Infinity Energy as well as energy from humans in Key Stones to power the rocket. It replicates the Energy from Mega Evolution and will fire the energy to create a warp hole to transport the meteoroid far away. They say this technology is similar to the teleporting portals that exist. The device that links the warp holes is a Link Cable.

They need one more Meteorite Shard and as they ask for that, Zinnia appears. She explains that the energy will cause history to repeat and that it is a bad idea and asks if you have a better idea. She will leave and Professor Cozmo will say you need to get the new Meteorite Shard from Meteor Falls, and Steven will leave

Go to Meteor Falls and go deep in it. There you will meet Steven and a lady who is a descendant of the ancient Draconids, an ancient people who pass down knowledge of Mega Evolution, and the lore of Lord Rayquaza, beginning of all. She explains that Hoenn has continually suffered disasters, and that the meteoroid is one that has happened on several occassions and the others are Primal Reversions awakening, and each time Rayquaza appeared to rescue. The leader of the Draconids went before a rainbow stone and made a wish which caused Rayquaza to change its body, essentially Mega Evolving. Mega Evolution was first discovered by the first meeting of humanity and Rayquaza. She explains that Zinnia is the Lorekeeper of the current generation. She explains how Zinnia tried to summon Rayquaza her own way by infiltrating an evil team and teaching them secrets to awaken the Primal Reversions to summon Rayquaza, and she is searching the world for Key Stones. Steven will leave and go to Rustboro City.

Go to Rustboro City and as you go to Devon Corp, you'll encounter a scientist being attacked by Team Magma/Aqua. Defeat the Grunt and another will come, and another. After they are defeated, the scientist informs you that Team Magma/Aqua have stolen the Link Cable and they are heading for the Mossdeep City Space Center.

Go to Mossdeep City and you'll bump into Courtney/Matt and some grunts as they go to the Space Center. Enter and you get a horde battle with the grunts. Five Mightyena with Intimidate and Snarl. Go upstairs and you'll face Courtney/Matt who wish to bring an end to the world. You battle Courtney and a Grunt at the same time. They have a Mega Evolution

Magma Admin Courtney	Camerupt
Items	Level 55
	Magma Armor Solid Rock
	Attacks: Rock Slide Yawn Earthquake Eruption
	Hold Item: Cameruptite

Aqua Admin Matt	Sharpedo
Items	Level 55
	Rough Skin -
	Attacks: Aqua Jet Taunt Agility Skull Bash
	Hold Item: Sharpedonite

Defeat them and Zinnia appears and takes the Link Cable from Courtney. She will explain about how there's a world just like this one but not the same. A Hoenn region exactly like the one they live in where evolution of Pokémon took a slightly different path and Mega Evolution is unknown and the war in Kalos never happened. She questions what if one day a meteoroid appeared over their world, what would happen to those people without the technology to stop it? She crushes the dimensional shifter. She insists that we can protect both worlds and steals the Key Stone from Courtney and runs off to put it with the Key Stone in the Magma/Aqua base

Go to the hideout and the grunts will say that Zinnia is too powerful but luckily their leader is deep in the base. You have to go through it again, battling various grunts. Reach the office and you'll see Zinnia facing off against Maxie/Archie and his admin Tabitha/Shelly. They have lost to Zinnia and Zinnia soon spots you and mentions you're the hero and here to save the world again, but saying you're too late, stealing Maxie/Archie's key stone and says that they can now summon Rayquaza and says that she hopes you can follow her. She leaves while Maxie/Archie gives you the Cameruptite/Sharpedoite respectively. Steven will then call and ask you to go to Mossdeep Space Center.

When you get to the Mossdeep City and meet Steven, he recommends you speak to Wallace at the Cave of Origin to break the seal of the Sky Pillar. When you get to Sootopolis, you will learn from Wallace that the tree outside the Cave of Origin was a gift from the "huge man who visited from the Kalos region", referring to AZ. He will then explain that only the Draconids can awaken Rayquaza and that he'll meet you at Route 131

When you get there, he will challenge you to a battle as it his duty as an ancient Sootopolitan. Defeat him and he grants you access to the Sky Pillar

Sootopolitan Wallace	Wailord	Tentacruel	Ludicolo	Whiscash	Gyarados	Milotic
Items	Level 55	Level 55	Level 55	Level 55	Level 55	Level 57
	Oblivious	Clear Body	Swift Swim	Oblivious	Intimidate	Marvel Scale
	Attacks: Water Spout Heavy Slam Earthquake Blizzard	Attacks: Sludge Wave Brine Rain Dance Dazzling Gleam	Attacks: Fake Out Scald Energy Ball Ice Beam	Attacks: Earthquake Muddy Water Rock Tomb Rain Dance	Attacks: Waterfall Crunch Ice Fang Stone Edge	Attacks: Dragon Pulse Blizzard Recover Hydro Pump
	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item

When you enter the Sky Pillar, you will meet Zinnia once more. She will point out the paintings in the Sky Pillar are the tales passed down for thousands of years and she will pass it to us.

Thousands of years ago, Primal Groudon & Primal Kyogre fought over the energy in endless clashes. Humanity could do nothing and had to watch as disaster swept over them. At that time, many meteoroids poured down from space and fell onto a waterfall that was home to a tribe of Dragon-type Pokémon users.

The meteors shone with a brilliance as if life was within and from that a Pokémon with an emerald hue descended from the sky. It was Rayquaza and its power overwhlemed the Primal Pokémon and returned peace to the world. Rayquaza was hailed as a saviour. 1000 years later, meteoroids fell again and struck the planet leaving a crater larger than any ever before. That crater become Sootopolis City

That meteor strike was the first of many disasters to befall humanity. The land cracked and pour a welling of natural energy beneath Hoenn, awakening Primal Groudon & Kyogre. The people made a wish for Rayquaza to return, and the meteor resembled a vast and powerful Key Stone. Rayquaza reappeared and as the people wished, a change occurred to the Pokémon. It transformed

Rayquaza confronted Primal Groudon & Kyogre and created a terrible wind that sapped their power, causing the two to vanish. It then flew high into the sky. A witness, a "tall visitor from a distant land", said "It is the Delta, born of the great disturbances in this world. By the bonds born of mankind's wish and the power of the stones, it will calm the troubles that plague the world." That was when the Draconids constructed the tower to hold the Rainbow Stone that granted Rayquaza the power and get closer to it.

A thousand years of peace followed that time but learning of the history's cyclical nature, the Draconids foretold that the meteoroids would strike again, and the meteoroid to come will be greater than those that came before and could break the world forever. The Draconids created a plan again to awaken Rayquaza in order to protect the world.

On the roof, Zinnia and her Whismur are watching the Meteor Shower at what they call the "Dragonhark altar" and are summoning Rayquaza to destroy the meteoroid. Zinnia mentions that she lost Aster, whom she named her Whismur after, and wishes to see her again. After the night, she asks you to take care of her Whismur if something happens to her and summons Rayquaza, however as she calls for the Mega Evolution, it doesn't work as her Key Stone doesn't react. Rayquaza has lost its power.

At that point, the Meteorite in your pack starts to glow. Zinnia states it is like a Mega Stone and Rayquaza grabs it, swallowing it. Zinnia says it did it to take enough power to Mega Evolve and take you on. This is where the capture takes place. It is Level 70. Rayquaza will wish to join your party on capture rather than be sent to the box

Zinnia teaches it Dragon Ascent and challenges you to assess your worth as the protector.

Lorekeeper Zinnia	Goodra	Noivern	Altaria	Tyrantrum	Salamence
Items	Level 60	Level 60	Level 60	Level 60	Level 62
	Sap Sipper	Infiltrator	Natural Cure	Strong Jaw	Intimidate
	Attacks: Dragon Pulse Muddy Water Thunderbolt Ice Beam	Attacks: Dragon Pulse Air Slash Shadow Ball Super Fang	Attacks: Dragon Pulse Moonblast Flamethrower Hyper Voice	Attacks: Dragon Claw Crunch Earthquake Stone Edge	Attacks: Dragon Claw Crunch Fire Fang Thunder Fang
	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item	Hold Item: No Item	Hold Item: Salamencite

Once Zinnia is defeated, she says the task is on you to beat the Meteoroid. Donning the Magma/Aqua Suit, you climb on the Rayquaza and fly up to the sky. You watch a cinematic in space of you on Rayquaza destroying the meteorite.

However, when the meteorite shatters, a black triangle remains and starts moving around. From it, Deoxys appears and instantly challenges you.

Defeat or capture it and you'll return to Sky Pillar and Zinnia's Whismur will give you a letter with Zinna's farewells. Celebrations continue around Hoenn. Wally mentions getting his Key Stone back and getting a ticket to a place from Norman. Team Magma reconcile and apologise, and intend to make a new beginning properly. Steven mentions how he wants to travel the world and see the truths of people and Pokémon, but will stay for the time being and fulfil his duties at the Pokémon League, but offers Wallace the opportunity to be his successor. Zinnia meets her grandmother in Meteor Falls who exclaims it's time for Zinnia to rest to make a new beginning and Professor Birch, Norman and your mother discuss how happy you and your rival are. Now at Mossdeep, you and your rival are watching the meteorite shower and then return home.