First enter the clock tower. Turn to the right. This guide assumes that you selected the pull emergency break function of the train incident. Open the door and you will be in the chapel, save, and proceed over to get a key that is the winder key and gun powders aa and bb. Then exit: as you do zombies will approach you and break through the window. Run in to the room across the hallway. Here you will meet Carlos again and will find some grenade launcher ammunition. Use this in order to fight off nemesis who will be after you soon.
Leave the dining room. Now you're in the main hall of the Clock tower. Here, if you go to both corners behind the stairway, you'll find to different music boxes. When you play them, you'll note that one of them is the correct melody, the other is off key. Try to remember the right one, you'll need it later. Now head to the room you haven't been yet, beside the stairway.
In this room you may find a few zombies. You will also see that there is a greenish door, which is stuck for now. Go through the corridor, it will lead you to the next room, which is a save room. Now keep going to the following door. Here, at Jill's left you'll see a picture about to fall of the wall. Examine it; you'll find a key. Leave all these rooms, get back to the main hall and then go upstairs.
Here you'll find giant spiders. You can evade them or kill them, but you must get to the door that leads you to the balcony. In the balcony, you'll see a button with a green light and beside this, there is a key hole. You'll need one of the keys you found before. Once you have used it, you'll be able to climb the stairs and go to the tower. In this room you'll find two items: a SILVER GEAR and a CRONOS CHAIN. In order to get the CRONOS CHAIN you have to use a machine that plays the song of the music boxes, but it's a bit off key so you have to make it sound right. Once you made it, the CRONOS CHAIN will be yours. Combine it with the key that has a hole to put another key inside and you'll have the CRONOS KEY.
With this key you will be able to open the greenish door downstairs. You should head to that room, but Nemesis will appear again in the balcony. Here you have two choices: "Use the light" or "Push him off". Use the light - if you push him off you'll meet him further on again. In the greenish door, use the CRONOS KEY and get in. You may find spiders in the corridor. Head to the next room.
Now, here you'll see a mercenary and a civilian, both dead. Beside them, three clocks: "THE GODESS OF PAST", "THE GODESS OF PRESENT" and "THE GODESS OF FUTURE". In this same room there are three statues with different types of gems in their hands that you must take: "Obsidian", "Amber" and "Crystal". Now you have to try them on the clocks, the clock of "THE GODESS OF PRESENT" must be set at 12 o'clock. If not, you'll have to keep trying. Once you made it right, get the GOLDEN GEAR and combine it with the SILVER GEAR. Get back to the tower and set the gear in the machine beside the item box to ring the bells.
Now you have to go downstairs, but before that, get ready for an encounter with Nemesis; he will infect you with the T-Virus, (once he infects you, you won't be able to check your health status in the status screen, so you should take a few green herbs or first aid sprays with you in case if Nemesis hits you too much). You're going to see a cut scene, then you'll have to fight Nemesis.