Have you checked the diary? What does it say? Are you using the latest version (10 or 9)? The first upload was bad. I can take a look at your save file, if neither of those help.
Viewing post in Coffee Story 20250608 Metaphysical Edition comments
On starting over I figured out what went wrong.
after the 1st lab (the tutorial one where we save yuri) I passed out and didnt go to sleep in my bed manually, it skipped the cutscene where we get TF'd into a girl with pink goo.
new save it did do that cutscene and is playing out normally.
if you want the save of that sequence break file, tell me where it is saved and I'll upload it. (but i am 100% sure it got bugged because I fainted and skipped the pink goo tf cutscene)