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Full Story
What follows is a scene-by-scene outline of all the bits of the TriHard Emerald story. This is the ideal end goal for the project; less important bits may have to be cut for time.
(Note: for the purposes of this overview, I will refer to the player character as male. But the player character can be either male or female.)
The player character is moving to Hoenn from the Alola region. Before he was our protagonist, he was part of Team Skull, and still wears some of their attire.
The truck he's riding in the back of stops and he hops out to meet his dad, who directs him inside the house and sends him upstairs so he's out of the way of the movers. "Go set your clock or something. We crossed a half-dozen timezones, so it'll need it." If the player comes down the stairs, the dad shouts from across the room to stay upstairs to stay out of the way.
When the player has set the clock, the dad comes upstairs saying that the movers are done and that he can come down now.
When the player comes downstairs, the dad is sitting at the table. Dad: "It's a nice place, don't you think?" [Yes/No, except it's "..."/"Meh"] "..." "Why don't you go meet our neighbors. I hear they have a kid too. Have them show you around the neighborhood."
Next door, the player meets Prof Birch's wife, who is a friendly person who overlooks any attitude the player character might have. She directs the player upstairs to meet her daughter(/son). Birch's offspring is just as happy-go-lucky as before, but is off put by the player's appearance like they're part of a gang. [The daughter's dialog is nearly identical to the original dialog, with slight tweaks for making her off put by the player's appearance. The son's dialog must be changed a bunch to have the same effect, and to remove things about being the gym leader's kid. Also dialog afterwards should be changed to indicate more awareness of keeping their pokemon healthy.]
The saving of Birch goes about mostly unchanged, and once they get back to the lab, Birch makes no mention of knowing of the player beforehand. He makes note about our great battling style, but asks that maybe we be a little easier on our Pokemon. When asked if we'll go and meet his kid, the [Yes/No] is [Meh/Nah], and he'll respond "Don't be that way" in either case. [The game saves here for the first time.]
Instead of the guy sketching out his own footprints, instead there will be an accident on Route 102 beyond the view of the player, and police officers and/or nurses will be blocking the way onto the route. If it is possible to have sprites off the map on the route, we should have the hints of something going on.
Officer: "Sorry, the road's closed for the moment. Please stay clear." Kid1: "Is it true some kid got mauled?!" Kid2: "Didn't he have a Pokemon with him?" Kid1: "Maybe his pokemon fainted or died!" Officer: "I said stand clear, please!"
[Brendan]
"Hey, little guy! How are you? Ok, so they live here too..."
"Oh! {PLAYER}! Don't scare me like that! I thought a Pokemon snuck up on me!"
"...Dad gave you a Pokemon? S-Sorry, I didn't mean it like that!"
"Sure, alright, let's battle. I'll teach you a thing or two about being a Trainer."
[battle] "...Wow, you're... pretty good."
"Wow, you're pretty rough in battle, aren't you?"
"Let's um... let's head back to the Lab, alright? I hear dad's got something for you."
[May]
"Hi! Aren't you a cutie? Wait! Where are you going?"
"Ah! {PLAYER}! You startled me! I thought a Pokemon snuck up on me for a moment!"
"Oh! Dad... gave you a Pokemon. That's nice of him! You helped him out?"
"Oh, yeah, sure. Let's battle and see how good you are!"
[battle] "...Wow... you're really tough..."
"Okay... do you really have to be so rough in battle?"
"No, no, I didn't mean... Let's head back to the Lab! I think Dad might want to give you something."
When the player arrives at the Lab, Birch and his kid are talking to each other. The player walks up automatically.
"Prof. Birch: Oh, hi, {PLAYER}! I heard you beat {RIVAL} on your first try! That's excellent!"
The rival suddenly storms out of the lab.
"Don't mind {RIVAL}. S/He has an extensive history as a Trainer already, so s/he was a little put off by his/her defeat."
"Here, {PLAYER}, I ordered this for my research, but I think you should have this Pokedex."
Player recieves Pokedex. The rest of the text is the same. Birch also gives you give Pokeballs.
As the player leaves town, their father stops them. "Oh, you've got Pokemon again, do you? Thinking of taking on the Hoenn League? [Yeah/Meh] ...You do remember why you were disqualified from the Island Challenge, right? [Yeah/...] ...Just... Go easy on them, alright? And be careful out there... You can always come home if you need to rest."
Now that the roadblock is cleared, you'll find the kids from before outside, discussing that they knew the boy who got mauled and they're worried for him now. Inside the Pokemon Center, the officer is comforting a woman who's crying over her son. There are people gathered around a corner bed in the upstairs PokeCenter, where the boy in question sleeps with one or two people standing over him watchfully.
When the player arrives in town, the exit to the west is blocked by Wally's mother, looking for him. She's positioned diagonal to the tree, and if the player walks on any side near her, she'll ask if you've seen Wally. Given a "yes", she'll ask you to go get him. Given a "no", she'll ask if you can find him. Either way she punts you back in the direction of town.
The sunglasses guy event is moved to just after this lady.
A man stands just outside Wally's aunt's house. He calls to her if she found him yet. This man blocks the doorway. "We're gonna be late..."
To ensure the player's party is fully healed before entering the gym, the door will be locked if the party isn't fully healed. "There's a sign on the door. "Closed. Back in 6 hours." Might as well pass the time at the Pokemon Center." The center will also have someone explaining the time passing feature of sleeping at the center.
The player eventually enters the gym. The leader inside will be talking with one of his trainers. The player can talk to him, though he rejects a battle with the trainer, asking explicitly "How many badges do you have? Come back when you have at least 4."
Then Wally will appear and ask for a Pokemon. The leader will say they don't just give out Pokemon here. The player character will make a motion, which will direct the Leader's attention to him. "You want to help him get a Pokemon?" Wally will then run up to the player and thank him, and drag him along outside.
The scene with the catching tutorial will play out pretty much normally, except that Wally will be using the Pokemon in the player's first slot. (Copied over and perhaps given 0EVs and 0IVs across the board). There's a high probbility the Ralts will faint.
[If Ralts faints:] When the game returns to the overworld, Wally is facing away from the camera. "Did I kill it?! Oh, no! It's still breathing! I'll nurse it back to health somehow! Com'on, little guy, we gotta get you to the Center!" He then runs away as fast as possible, leaving the player behind.
[If Ralts is caught:] When the game returns to the overworld, Wally will be extatic and thank the player, and run off, leaving the player behind.
The player regains control from this point. The gym will be empty when he returns. Wally's mother will be inside the Pokemon Center near Wally, who's either trying to heal the very hurt Ralts, or healing Ralts a bit for them to be ready to journey. The mother seems a little miffed about it.
The man in sunglasses event is unaltered, save for a line change after he calls the player an ordinary kid. "Woah, alright, you're a Trainer! Calm down! I didn't mean anything by it." "I'm sorry to have taken your time. {SMALL}Jerk."
The player comes across a random researcher in the middle of the woods who's looking for a Shroomish. After he asks, the player gets a choice between [Nah/Meh]. But the outcome doesn't matter because a Team Aqua grunt attacks and the player gets dragged into a battle. The dialog is unaltered before the battle.
"Grrr... you've got some nerve meddling with Team Aqua! Come on and battle me again!" "Stop laughing! I know I'm out of Pokemon!" "Whatever, I gotta get back to my posse anyway. Gotta get that thing in Rustboro. I'll let you go today!"
Seeing as HMs are getting cut (lol), the Cutter's House will give you the TM Cut and allow you to use the Cut capability, once the gym badge is won. The dialog here will have to change to match that.
Scott's dialog in the Trainer School will have to be altered to reflect the new mechanics.
First thing the player might notice: the sign on the front will have a list of "Roxanne's Certified Trainers", where the player's name isn't on the list. But a whole lot of other names are. When the player beats the gym, the text of this signpost will change... to indicate that the player still can't find their name on the sign.
...
The progagonist runs into Birch's kid on this route. They battle, and at the end of the battle*, the Protagonist's Pokemon deals a critical hit to the Rival's starter Pokemon. The battle end with the Rival shouting his starter's name.
The after battle dialog has the rival's back to the protagonist. "[Starter]?! [STARTER]?!?! What did you do to [him/her], [playername]?! [Starter]! Wake up!!" And the rival runs away quickly.
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