Pretty much just what's going on in the present time.
Like why is half the team in some random location and why I thought the protag already met the yakuza figure so why would it be dangerous for him to meet him again
1) I guess Tokyo Fist got the same intel Goudou's mercenary group got and they both went to investigate this base of Dark Services Providers. It might have been a bait. We will see.
2) The protagonist met only Kakine, the guy who reads minds. He is a capo, to speak in mafia terms. The boss of a group that's called Adou group. It's one of the groups that are under the yakuza outfit called Gojukai.
The stalker went into Gojukai headquarters, the headquarters of the main family and of Big Boss himself.