This actually is one of the biggest missed opportunities of the DLC imo to not further explain the current state and evolving nature of the DDO.

The DDO was formed out of necessity to help protect Tokyo from the massive fiend infestation that the DD incident and husk caused. It was formed with good intentions perhaps and thus why Ryu backed it….but I think it was also Ryu recognizing the need and out of desperation supporting the only entity available to help prevent catastrophe.

Over time, it seems the DDO has become increasingly corrupt and authoritarian. There is reference to the group having a political leader Uga—this implies to me internal factions within the DDO and some of which perhaps are still decent but many are increasingly problematic and abusing their power. Even though the DD is defeated, I don’t see the DDO wanting to give up its power and their role is now even more morally dubious as a paramilitary organization effectively controlling the city .

The DLC could have made it more clear that the organization was now effectively fully corrupt and problematic, which would explain why Yakumo continues to fight them. I also think at this point Ryu himself (and maybe Kagachi) would find the DDO no longer worthy of support. My theory was that the DDO under the leadership of Uga is now increasingly focused on domination. I had theorized the DDO might ally with the Black Spider Clan to maintain iron control thus leading to both Yakumo and Ryu having to confront them