Ideas

List of Ideas:

Black Fog - Farming Network
http://bulbapedia.bulbagarden.net/wiki/Black_Fog

A pokemon that commands a group of gastly, drowzee and Hypno. It is huge in size, completely black unlike the normal Haunter, and uses the gastlies to conquer different areas, villages and cities. They put pokemon and people alike to sleep, and when they do, they remain in a coma-like state and their vital functions drop. The black fog then casts dream eater on them, stealing their dreams and lifeforce. Its size increases with this, which is an indication of growing stronger. Its goal is to evolve, but the talking gastly from the anime has evolved into gengar first, so it commands the more powerful hypnosis network.

Hypnosis network
Instead of killing humans and non cursed pokemon, some cursed ones will take over whole towns and villages. This is a, putting them in a magical come, and slowly draining them of their souls. This will happen at some point ina village Vergil and Cole will visit, which will be attacked by a cursed Hypno. Later, Black Fog,the talking Ghastly and even Darkrai will be revealed to be behind this operation. Black fog will have also imprisoned Sabrina and will feed on her and her pokemon's souls, which wil make him immensely powerful. Vergil and Cole will find out the source of its power, and will use worry seed on Sabrina's pokemon, waking them up. As a result, Sabrina will wake up too, and Black fog will be defeated and destroyed.

Volume 2 details
Brock sends two groups out there. One at Cerulean, which he leads himself, and another one to viridian, to ask for help and alert them and indigo about the incident in cerulean. He finds misty dead in Cerulean, and the group heading to viridian is returned dead. The only survivor says they allowed him to return to tell them that team rocket has taken over viridian and no outsiders are welcome. Brock then sends Forrest to inform the pokemon inspection agency, but Forrest is killed in the process by cursed pokemon. Brock then decides he should barricade the city and not sed other parties out there.

Trainers:

Solidad (Pdgeot, Lapras, Slowbro, Butterfree)

Pete Pebbleman ( Cloyster, Arcanine)

Dark trainers
There are many guilds of trainers in the wild. Most of them can be categorised in the following:

Dark guilds. These are groups of trainers who attack villages, settlements and remote people who hurt others for their own good. They may even go as far as kill others.

Corrupted guilds. The members of these guilds have fallen to the curse as well. In order for a human to fall to the curse, they have to be invited by another fallen human or talking pokemon. The trainers become shadier and obey to the darkness. In return, the cursed pokemon do not harm them. They all describe it as "their dreams come true".

Trade City
Vergil will go to a city for help against the Saffron attack, and he will find out that in that city they heavily relied on importation to feed the populance, therefore they have a big shortage on supplies right now. In order to help them, Vergil will help the city by investigating the matter. They nearby commerce city will be visited afterwards, and the people there say that ghost pokemon attack them on the street at night, therefore they can't trade with other cities. Following the trail, Vergil will defeat the talking ghastly and disorganise the cursed pokemon behind these attacks.

Pokemon Ninja School
It is an academy using ninja pokemon, specializing in training speed. Ash thought they would be perfect as allies for the assault on Saffron, and Vergil was sent to ask for help. The people there accepted, on the grounds that Vergil stay and train with them, after seeing his pokemon's potential. They said Vergil was a good trainer, but he needed to become stronger and more agile himself. Vergil agreed, wanting to become stronger, and for a time he stayed and trained there. The Ninjas acted as the elite infiltrating unit during the invasion of Saffron, but due to Ash's betrayal, many of them were killed.

Also, since many former ninjas used poison and dark pokemon, they became dark trainers. Some of them infiltrated the school again, and under Ash's orders stayed dormant until the battle of Saffron.

The reason Ash sent Vergil to train there was first to become stronger (Ash was planning for Vergil to side with him after the battle of Saffron and travel the world together). Also, he wanted Vergil to get out of his way while he was planning the sabotage of the whole attack.

It turns out that the leader of the Ninjas (Janine) is the mysterious dark trainer with the weavile.

Vergil befriends a young ninja trainer from there.

Giovanni's death
During the battle of Saffron, when Ash's forces start massacring the trainers, Giovanni and Jessie watch from atop, and Jessie is confused. Giovanni tells her that this was the plan all along, and although he was supposed to kill her, as she is a strong trainer, he wants to offer her the chance to join him. Jessie denies and asks how he could do that, and Giovanni replies that in life there are bigger things than team rocket. He tells her that the enilightening power can give her whatever she wishes, and her negative emotions will all go away.

Jessie still rejects the offer and preparess to fight, although they both know she is no match for him. After they start their fight, Jessie's first pokemon is defeated by Persian, and when Persian is about to deal the finishing blow, Arcanine appears and slices its neck. James appears from a corner, and says that since he abandoned his last double battle with Jessie, they are still in a double battle, and declares that Giovanni will have to deal with them both. Giovanni is enraged by the death of his cursed persian, his favorite pokemon, and swears he will kill both of them.

Giovanni loses, and one or two things happen:

1) He is just killed without the involvement of Mewtwo.

2) Mewtwo is his last pokemon but kills him, and helps teleport some grunts out of there, saving them.

After Ash's betrayal
Aftermath of battle of Saffron

Moltres fire
In the championship, the moltres fire lit at the beginning symbolizes peace and co-existence between the participants, and every living person in general. After the battle of Saffron, the championship happens again, and the fire is lit by Moltres' dark fire, which symbolizes coexistence between cursed people and pokemon. When Vergil is in Johto, he makes a plan that he must light the championship fire with a fire from a non-cursed legendary fire pokemon, and this way he and the other non-cursed trainers can take part in the championship, since no one will be able to hurt them outside the championship. They do so, and he reaches the finals where he fights Ash and wins. After that, the championship ends and the other trainers take up the fight against other remaining legendary pokemon and win, freeing kanto from the darkness.

Tournament of the champions
It is revealed that a tournament took place in which Ash was a dark trainer and those he defeated turned into dark trainers as well, along with most of their pokemon, or were killed. As a result, the strongest trainers of the world have turned to the darkness, and only those who were defeated by them are uncorrupted. Some of these trainers are imprisoned, like Gary Oak (maybe Gary isn't, but others are)

Blaziken
Vergil will catch a blaziken after training at the ninja village. The Blaziken will be very hostile against him, realising Vergil is Ash's son, but in the end will like him, after espeon links the two of them together and blaziken sees how Vergil's mother also died because of the darkness. It will be revealed that this Blaziken is May's blaziken.

Don't know yet if Vergil or Cole catch it, but May won't die by Ash