We'll see how this works out in the next, final volume.
For now riddle me this: What was the military thinking? They heard that Gotou will go after Shinichi.
Perfect opportunity to lure him into an ambush with snipers, flamethrowers, poison gas, autocannons and so on. Shinichi's insides can be laced with cyanide capsules in case Gotou eats him.
Did they just give up?