There’s not really a huge mystery (multiple cases) in this so I apologize but it’s really good: https://www.mangago.zone/read-manga/mystery_to_iunakare/
Also here’s this the mystery shapes the whole manga/plot: https://www.mangago.zone/read-manga/billion_dogs/
Not sure if this one counts as a great mystery plot for your taste but here you go "The Player That Can't Level Up"
https://www.mangago.zone/read-manga/the_player_that_can_t_level_up/
Thank you guys!! I'll be sure to read them ^^
Can anyone recommend me a mystery manga with a huge overarching mystery in the story?
Either gender MC is okay, preferably no romance or harem please