So, the Professor you're looking for is at a lake near the second town? Because the description you have in the story summary is a little confusing.
*EDIT*
Two other things - do you have the starters set, or are you still trying to figure them out? Not that it's really that important for a plot writer, but I'm curious. And what generation are we working with?
Because, if the Professor has visited a Volcano, a Swamp, and a lake, the pokemon he would have with him (if he caught pokemon during that excursion, which feels likely taking the circumstances of the plot, at that time, into consideration) would have to have certain typings. For example, to me, 'Volcano' says that the fire starter (if you plan to follow the fire/water/grass pattern) would either be full fire or have a rock or ground subtyping, 'Swamp'; the grass starter would have Water, or maybe ground (if a grass/ground pokemon even exists) subtype; and at the Lake, well... that implies to me that it could very well be any of the water types that exist, really.
Again, not that this is important to a plot developer/writer.
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Alright - I've been doing some thinking, and this is what I've come up with for the forest event. Can't say how the meeting with the Professor would go, but I was thinking only about the forest at the time.
When you're navigating the forest that first time, you probably won't have pokemon - that's why you're risking the forest to get to the professor, right?
For an event, and the introduction of one of the evil teams, you come across the grunts; perhaps as they're managing their cargo. But before they notice you, a trainer charges in from the opposite side of the clearing (if there is one)
I was thinking that perhaps this trainer winds up being a rival, that maybe he's trying to getting something form the grunts - maybe they stole something important to him - but either way, he wants something the grunts have.
This can work as a distraction for the player, allowing them to pass without having to write around fighting, as you have no pokemon to fight with. You could have it so that the grunts notice you, and by extension the other trainer, who refuses to let them change the subject - perhaps he's bent on beating them, and confident that he will beat them and get the thing he wants; he doesn't think you, a pokemon-less little girl/boy, are important.
Here, there could be a script that forces the player to run away, forwards (or whatever direction moves you further in) and out of the cargo-filled clearing - another script could be placed to prevent the re-entry of the clearing.
I was thinking that the forest exit could let out in a route leading away from the second town, perhaps a shorter route, with little to no grass, that leads to the lake the professor is at - like the trail to Lake Verity in the D/P/P gen.
When you get back to the clearing the grunts were at, you could either have it so the grunts are just finishing trainer off, or that you come in after he's already been beaten, and are taunting him about how weak he is, or something.
They notice you, some banter is tossed about (maybe some from the Trainer, possibly proclaiming that you are gonna get flattened, as he got beaten and was a trainer long before you were?)
You fight, you win, and maybe you talk with Trainer about how you beat them, that you're really good for someone so new to such a thing? Afterwards, perhaps the Legend you mentioned shows up. The two of you look at it, it lingers for a few moments, then leaves.
I'm not sure what relevance this would have in the game, but it might be a way for Trainer to show up again - perhaps he's never seen that pokemon before in his (or her) life, want to hunt it down. You could re-encounter him multiple times throughout the game.
Granted, this makes the Trainer very similar to Eusine from G/S/C, but I'm still uncertain about how else to get him to show up multiple times.
But, do you like the idea? It doesn't feel too far-fetched to me, not too out-there.