The Watchdogs (番犬 Banken?) is a unit under "Tokyo" meant to assist in security measures regarding the Irie Institution. They consist of trained professionals in military combat from the SDF and are intended to be called only in extreme circumstances. They have access to a wide variety of military supplies and vehicles as opposed to organizations like the Mountain Hounds.
In the original visual novels, Okonogi laments on how he would rather be in charge of the Watchdogs instead of the Mountain Hounds for several reasons; one being the Mountain Houds' incompetence, and the other being the fact that the Watchdogs engage in more combat situations than the Mountain Houds do. Okonogi's tendency to think carefully about a situation instead of jump in and be ready to engage in combat is the reason why he was assigned to the counterintelligence squad.
The Watchdogs only appear during the ending of Matsuribayashi-hen and Miotsukushi-hen, just as the Yamainu are considering retreat and soon surrender. The combat forces rush in and overtake the Yamainu, making them willingly surrender. They were called in by Jirou Tomitake after his escape to Okinomiya. In Matsuribayashi-hen, the Watchdogs surround Miyo Takano in order to arrest her, but Tomitake interrupts them. In Miostsukushi-hen, however, they actually try to shoot Takano before Hanyuu takes the bullet and saves Takano.