The army has attempted to attack Innsmouth, but they've become mad upon approaching the main temple. You're sent with an escort of a few marines to an old smuggler tunnel.
After being briefed by Sergeant Sam Carter, head down the steps and walk to the end where a rope is being setup. Climb down - and notice that the ice starts breaking apart. Run along the white section of the river until you reach the pathway to the tunnel. You can see a savepoint painted on the left wall.
At the end, you will meet with Private Joe Parker, who asks you to use the flamethrower to melt the door. He opens it, but is attacked by a Deep One. Follow the deep one at a moderate distance, and lure him towards the door outside. When he is at the door, turn on the flamethrower to burn it.
Tunnel and prison
Enter the tunnel - you will see the remains of Parker. There is also some dynamite you can pick up.
The first path to the left leads to a series of cells, and where you can get a bolt action rifle and a large bronze key. You will also meet with Agent Lucas Mackey, who says there's some sort of ritual going on upstairs, and also see another prisoner who has since lost his mind.
The other exit leads to the temple, but is blocked by hostile starfish. Place the dynamite next to the barrels of rum, and take cover. The blast will eliminate the starfish and open the door.
The game autosaves. Head up the spiral staircase, and you'll reach a back room in the first floor of the temple. You will want to enter the door on the right to collect a knife, and push the bookcase to reveal a secret passage containing two medikits. This allows you to use a one-way door to sneak up on at least one of the Innsmouth hostiles, and kill them before they can react.
From the secret one-way door, you will want to follow the left wall, which leads to an office who's other exits are bolted shut. You can get a key, which unlocked the first door on the left from where you entered the temple. This leads to a storage room that allows you to reach the second floor through a trapdoor.
From the trap door, one door on the side brings you to a room overlooking a few enemies. Entering the room will also activate enemies that approach from behind, which is just in time for you to use the shotgun laying on the ground. It contains a winch to raise the floor in the other room, but you need something to lock the mechanism in place.
On the second floor on the side of a staircase is a back room. The room contains the diary of Robert Marsh. Smash the window in the back room to see a ghost of someone you failed to save. From here, you can enter the other room where you can see the prayer to Dagon (which you can't read yet), and unbolt the door for easier access.
You can return to the first floor by jumping over the furniture by approaching from the right-hand staircase, and climbing the chairs on the back of the shelf. Locate the safe in one of the first floor rooms, and enter the combination 1878 (as found in the Diary of Robert Marsh, and turning right first). You can find a scroll (the prayer to dagon), Mackey's pistol, and the Ponape scripture. Return to the room on the second floor containing the inscription, and decode the prayer. This allows you to use the staircase between the first and second floors, while accessing the room containing the passage to the basement. In this room, you can get the key to Mackey's cell on the podium.
Return to Mackey, give the key and pistol, and head to the winch using the staircase you opened (Mackey can't climb ladders). Cultists will repopulate, and you will have to fight them once more, although the first one can be killed with the knife. Once Mackey raises the podium, you may head downstairs.
The basement has Robert Marsh and two sorcerers performing the ritual. When it is interrupted, a wind will pin you against the doors, and you will have to shoot the two sorcerers while dodging their attacks. The wind stops once the sorcerers fall, allowing you to examine the room.
To proceed, you will need to enter a combination on the back of the three statues. First, read the tablet on the right to learn you need to bow at the statue of Dagon, which contains a key that you should write down. On the stone tablet to the left, note the symbols from top to bottom as if the two fragments on the ground are in the proper position. Convert this to a combination, where you press the buttons in Dagon, Hydra, Dagon, Cthulhu, Dagon and Cthulhu.
The door opens, and you can head down the tunnel, but the ground collapses before you can catch up with Marsh.