After you defeat Nicholai, he will retreat into the clock tower and leave your battle for another day. You will receive orders to collect the final EMP and use it to take down the power plant so that nobody will be able to radio for help. That way, word of the infection won’t spread to other parts of the country. This plan may be destined to fail in the larger scheme of the RE canon, but you’ll still have to give it your all. If there is any ammo left on the ground, collect it and reload (you may also want to swap out your Semi Automatic Rifle for something with a higher rate of fire, since you will be fighting a ton of enemies ahead.)
The clock tower door will open ahead of you. Enter the clock tower and head towards the piano belting out a familiar tune. As you approach the piano, pull out your gun. Shoot the bodies lying around the piano; if you don’t, they will rise and attack you as you pass by. Killing them now, while they are defenseless, is easier. Head through the secret door opened by the piano’s tune to get to the next room. A group of zombies will be in this room. Grab the third and final EMP from the altar. Turn to the left and shoot the trip mine. Head through the corridor that the trip mine was protecting and collect the Intel from the table. You can also pick up a Pump Action Shotgun here. You will radio Umbrella HQ and inform them of your success. As you do, a group of zombies will burst in from the side door. An explosive zombie will be mixed in with the hoard of regular enemies. Aim for this zombie first. If you are lucky, you can blow him up and take out the rest of the wave with him.
When the wave of zombies is dealt with, leave the church area and head towards the back of the clock tower. You will find a small doorway here. This will lead you to the alleys behind the clock tower. Leave through here to reach the next area, back out in the streets. Be ready to switch your focus from zombie fighting to battling the Spec Ops troops. Equip your Stun Grenades and prepare for the arduous series of battles that lies ahead.