There's a connection between the disappearance/deaths of Ash Ketchum and Gary OakThink about it. Assume that the comic takes place in 2009. Kahn mentions that Gary disappeared ten years prior. The date on Ash's statue? 1981 - 1999. 1999 being 10 years before the comic, the same year of the other's disappearance. The two incidents are probably related.
Masked Dude IS Gary Motherfing OakNot sure of his motivation exactly, but basically he roams the land now punishing other 'Gary Oaks', seeing as how he does specifically go after Atty who he identifies as a Gary Oak, even with a speech about justice. Could possibly be as atonement for being the original example of it, if coupled with the above WMG then this could be triggered by Ash's mysterious death.
The Masked Man is Ash.If the disappearances are connected, then it may be possible that both bodies were never found. It's just assumed that both are dead. However, it may turn out that Gary really did die, and Ash is so consumed by guilt at failing to save him that he could never bring himself to return home (out of shame and out of fear of confronting Prof. Oak about what happened). He's spent the last ten years taking his anger and frustration out on whoever he deems to be an abusive trainer: trainers who couldn't care less about their Pokémon, who only want to use them for fighting, and who purposely target weakened or helpless trainers. Unfortunately, years of bitterness have hardened him to the point where he's not above completely devastating the Pokémon of Jerk Ass trainers. As for where Pikachu could be in all of this . . . maybe Ash lost him, too?
The Masked Man is Daisy Oak.Her brother and famous neighbor are missing, her grandfather's gone loopy... where else could she be?
We might find out more of the backstory when Atticus reaches Pewter City.Unless the Gym leader has changed, Atticus will face Brock, who happens to be one of Ash's closest and oldest friends. There might a possibility that he could end up hinting at what happened with Ash and possibly Gary.
Dragonthing's going to go through a very rebellious stage upon evolving.Probably not to the level of "I SWEAR TO GOD WHEN I EVOLVE I'M GOING TO KILL YOU ALL", but enough that Atty's going to realize just how much he took DT's Undying Loyalty for granted.
The Masked Man is GoldHe has a Feraligatr, one of the Johto starters. But in Gold and Silver, when you reach Kanto, your Pokémon should be way more powerful than everyone else's. But the Kanto trainers are somehow level 50-ish. Obviously, if Gold really went to Kanto after beating the Champion, he would be about as powerful as the Masked Man seems to be. Also: Black hair.
Jessie and James have taken over Team Rocket....and that's why all agents have to recite their motto!
George is either a relative of the Masked Man, or she is the Masked Man.Chapter 6 reveals she has either his mask or a copy of it. Seems Gabe is popular with the ladies and a lot of people have copies.
The Masked Man is RumpelstiltskinIt's obvious. Many of H0lyhandgrenade's characters are from other comics she did. Rumpelstiltskin from her other work (he's an exact copy of him in every way) may not be Gabe and vice versa as stated by H0ly herself, but it's not impossible.
None of the anime or video game characters will make an appearance.Besides the Nurse Joys, Officer Jennys, and Professor Oak. None of the main characters of either version will appear just so H0ly can avoid any controversy with them (she would have to change their personalities to match their new ages and she's already stated that she isn't interested with sticking to the lore of Pokemon). All the gym leaders will be different and maybe the old ones will be mentioned in passing as being dead, missing, in jail, on vacation, insane, in retirement, etc.