The first three big boss battles are all part of the long "Crumbletown" story arc that makes up the first part of the game (up to Slateport City, in Ruby terms). We had small hints of another story arc, involving Freya the Pidgeotto's past and the mysterious "round thing" she was so obsessed with, but that particular arc doesn't fully start to come into focus until close to the end of the Crumbletown arc. Anyway, as we saw in the screenshots from last time, you meet up with a skittish Beautifly named Doppa as you travel along Golden Trail (equal to Route 102 in Ruby terms). The reason she is so skittish is because her son, Peppo, had wandered off - and never returned. And the residents of the forest know all too well what that means - he was probably kidnapped; hauled off to dig through the Magician ruins in a terrible place to the north called Crumbletown. Getting Leppo back doesn't necessitate going all they way up there - though you go up there anyway XD - to rescue the little Wurmple, all you have to do is corner and defeat the first of the bosses in a place called Ratkarat Cliffs (equal to Rustboro City).
Boss Argo
Species: Vulpix
Specialty: Scaring defenseless little bug-types with his flames
Argo is unique in that you battle him more than once - you first catch up to him in a place called the Gorshi Swamp (equal to Petalburg Woods). Defeating him won't save Peppo from his clutches, however - he runs off and you'll need to chase him up to the Cliffs, corner him in a tunnel, and battle him again in order to save the little Wurmple. Beating him the second time silently enables - as in, there's no big fanfare or announcement like you get with beating a real Gym Leader - the use of Flash in the overworld. And yes, he is a cute little Vulpix - I see no reason why pokemon need always be pigeonholed in terms of behavior and personality based on their species. ^^' Cute pokemon can be rotten and ugly pokemon sweet - but ugly pokemon can also be nasty and cute pokemon be friendly. It all depends on the individual. XD By the time you fight him, you'll have 1 team mate besides yourself - Mjolnir, a Raichu - and a travelling NPC who does not battle - Doppa, the Beautifly.
Boss Cragclaw
Species: Skarmory
Specialty: Capturing slaves and helping to fulfill the mad dreams of his Lord
The next boss you meet is a species not generally known for gentleness - a Skarmory with bloodied talons known as General Cragclaw, in a yet unnamed location that in game terms is equal to Dewford Town. Cragclaw is the yes-hand man to the "Lord" who rules over Crumbletown as his own. Defeating him silently enables Rock Smash on the overworld. What he is doing - other than working under the Lord's employ - is not entirely worked out at the moment. In short, he's all sprited up but with nowhere to go quite yet. XD By the time you fight him, only Mjolnir is with you.
Boss Hufsa&Kik
Species: Stantler and Natu
Specialty: Lord and Assistant, respectively - but is it really that simple?
The next boss are actually bosses, plural - the Lord of Crumbletown, Hufsa the Stantler; and his yes-man who may be much more than that, Kik the Natu. There's more to the Hufsa/Kik dynamic but I am not going to spoil it for you :) Crumbletown is also a place filled with deep mystery, and a tall tower, and strange stone figures - along with slaves, and old tires and soda cans and pipes and trash - and I would like for it to keep its mysteries until the game's beta release. ;) What I will say is that Crumbletown's tall tower has something at the top of it which raises a lot of questions about how the world had once been...and awakens a deeper mystery, about why things are, now, the way that they are. For this game is not only about a quest to head north and beat the biggest big bad and keep it from ruining what's left of your world - it's also a quest to discover the mysteries and secrets around you...
By the time you battle Hufsa and Kik, you have a second team mate - Violet, the Rattata. Another recruitable character - Vann, the Minun - is following you but is in a role just like Doppa the Beautifly's above in that you cannot take him into battle at this time (you can later, though). Beating these two silently enables Cut on the overworld.
The next group of bosses are still nebulous as I cement together the next major plot string (and the next plot string after that) - since my work is currently on the Crumbletown arc I've had a lot more time to think about it and plan things, while Freya's arc and the Northernlands arc are less developed (though I certainly have ideas in mind). An Elite Four equvliant has also not been developed yet, but there are three different champion equivliants, once of which - the final, final boss - in true RPG fashion has two separate forms and you have to beat it twice. XD I do, however, have one more NPC to discuss...
Stranger Aspen
Species: Pikachu...sort of
Specialty: Being spooky
Aspen (his original name was Rowan, but I changed this for the obvious reason he's not supposed to bring to mind images of an old-fart professor from Sinnoh XD ) is a scruffy, fluffy, one-eyed Pikachu wearing a bandana you meet at times during your journey. Who is he and what does he want? What is the source of his mysterious knowledge of the time long ago? Why does he never join your team - despite his visits and interest in you - and why is he frightened of being touched? Is there a connection between him and Mjolnir, the Raichu travelling with you? (Of course, me bringing it up means there must be XD ) But that, and the other points, are mysteries that will have to be revealed in time...