so starting from the part where they separate because of Kuze's dad being brought down by the yazuka, The Yamamoto Group. Kuze (seme) disappears and Shimojou (uke) joins the yakuza. Shimojou joins the Yamamoto Group and Kuze becomes a police officer who is now investigating the Yamamoto Group. Shimojou finishes his job where he threatens a politician (who I believe contributed to Kuze's dad suicide otherwise why would they mention him being a politician who brings down his rivals) and unexpectedly reunites with Kuze.
Shimojou and Kuze engages in a pet/master relationship. Shimojou finds out that Kuze is a police office and finds this to be boring because of the simplicity Kuze went around dealing with the Yamamoto Group. Based on their past, Kuze probably wants revenge on the Yamamoto Group for his dad and Shimojou probably wants to trash the Yamamoto Group for being the reason for Kuze's disappearance in Shimojou's life (we know Shimojou wants to trash the Yamamoto Group because in Chapter 3 the author shows that he still kept the newspaper article where it talks about Kuze's father's suicide). They both want to trash the Yamamoto Group but Shimojou chose to go the scumy and risky path while Kuze went to the normal path which Shimojou comments on it being boring because of the simplicity/normality of it.
So to spice things up, Shimojou decides to start leaving clues on the Yamamoto Group for Kuze to find. Kuze finds them like Shimojou wants and is able to bring down the Yamamoto Group. Shimojou expected Kuze to arreset him but Kuze knew he was giving him information on the Yamamoto Group on purpose so he didn't arrest him and well they sorta confirmed their love for each other.
However these fellas gotta have thrill in their lives. So the game of hide and seek starts. Kuze runs away with Shimojou's money to another country. Kuze probably thought this little ruse would trick Shimojou into thinking he had retired from the police but Shimojou is too smart for that. Also Shimojou is hiding now because he is the one who leaked the information on the Yamamoto Group so he gotta keep a low profile and he is also hiding from the police as well. But after a year, they decide to go back to Japan to capture the Yamamoto Group's yakuza rival. With Shimojou working on the inside by infiltrating the rival yakuza while Kuze goes back to the police.
So what ends up happening is the Shimojou is Kuze's confidant for things regarding the yakuza. So these two are going around capturing the evil guys.
Flaver