When you are ready, head to Dragon Command and all players should stand on the grate where Sophia was. You will be dropped into the sewer and out towards the boss arena.
A dragon will spawn in and occasionally light up the arena. You will need to hold out your shield to survive in this fire without damage. Eventually the dragon will perch on top of a building with an orange glow on its wings or chest. You must shoot this glow to damage it. If done enough, as it flies Nikolai will damage it further with his mech to open another weak spot.
Avoid dying by zombies and Manglers during this fight, and the dragon will eventually die. A short cutscene will start before you must face Nikolai.