Uh, its a bad idea to try to just skip to the gym as you can break cutscenes and who knows what can go wrong due to absence of some triggers in the game.
Soo yeah, in order to get to the gym, you need to go to tourmaline station, to the desert, then finish the train puzzle, and it should be clear from that point :).
https://docs.google.com/spreadsheets/d/1NmNBklcSI_OqWKMAaJ_WyqjBJ5J7lo3IuwTftIaJlIw/edit#gid=1480144547
the excel spreadsheet, you can add passwords when prompted by Ame or at a PC with a data chip.
PS: Passwords are modifications to the game and you don't necessarily need to use them, just some QoL upgrades and preferences.
you don't have to walk up the stairs, right, look down, one step down and two steps LEFT, three steps up, touch once, one step left, two steps up, turn down, finish.
I started from scratch and have finished up to the final boss, and I can confirm that this game is an absolute masterpiece.
Please devs, take a break, you guys deserve it after the hard work you put into this game, I waited for it to come out for around 3 years, and the wait was so worth it.
YOU ROCK DEVS!