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The Cult's House
Things are pretty tense at the cult's house. The police have it surrounded but want Jack to go in as a negotiator, as per the cultists request. Follow the officer up the steps. You can stop and talk to the cops along the way for a little background. Once you make it to the top, Nichols will point out Victor Holt. He's hidden in the alley to the right of the building.
It doesn't matter if you sneak. As soon as you step out into the yard, the cultists will get trigger happy and fire on the cops. Two will go down and there's nothing that you can do. The rest will step up and counter the riflemen, but it isn't really your concern. Victor Holt ran inside, so Jack Walters should probably follow if he wants to figure out why he's so important to them.
The room on the left side has absolutely nothing of interest. Just some old food and supplies and a few rats. The room on the left is their sermon hall though. Look around the room and walk up onto the little stage. There's a long note that appears to be Victor Holt's previous sermon. Use the action key to read it and then pick it up. This will be the first clue. Walk back to the hallway and follow it out to the stairs. Jack will stop and make a note of the strange symbol in the corner. This minor Elder Sign is just a chance to save if you want to do so.
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Investigating the Cult - A Living Member
Walk up the steps to try and find a few surviving cultists to capture or interrogate. Look in the first room on the left for a dying cultist. He'll say a few words to you before he goes. There's nothing to really investigate though, unless you want to have Jack examine his body to confirm that it's covered in tattoes and recently dead. The shotgun shells are all spent, so you can't get a gun either.
Walk down the hallway into the next room on the left to find a surviving cultist. Unfortunately the police manage to wing him right as he's about to explain everything. The shells here are spent too, so no weapons for Jack. Examine the body, grab the key off of the chair and walk out the door to the room across the hallway. This bunker/large bedroom is now empty. It seems that most of the cultists decided to take their own lives. You can examine their bodies to confirm that it's a mass suicide via poisoning. Note that staring at the bodies really bother Jack. Staying in the room has a fairly steady drain on your sanity.
Look on the main table for the only thing of true interest. There's a diary on the table. Pick it up to get your second clue.
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Investigating the Cult - Locked Rooms
Since we have a new key, go back down the steps to the two locked rooms on the first floor of the cultists' home. It doesn't unlock the door across from the stairs, so walk to the right and unlock the second door. Step into the study and look around for a bit. It seems that the cult really liked Jack...really liked him.
Seeing all these pictures and stalking evidence really freaks Jack out, so try to grab the key off of the desk quickly so you can walk out and regain your composure. This key opens the other door.
Go into the new study and listen. There's a lot of screaming going on somewhere else in the house. Before you investigate it, walk up to the desk in the corner. There's a slightly glowing manuscript in the open desk drawer. Look down and open the drawer up to reveal the rest. Pick it up to gain another clue and your first Mythos manuscript.
Walk toward the mirror until you drop off into a partially hidden track on the other side of the room. Look at the floor in the corner to reveal a trapdoor. Go down it to enter the cult's tunnel system.
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The Cult's Tunnels and Yithian Technology
Walk through the tunnels and try to move at a steady pace. Some falling beams will take out the cultist ahead of us, so that's one problem out of the way. Keep moving. Some more beams will fall but they shouldn't bother you. You'll eventually make it out of the tunnels and enter a very full morgue. Examine a body quickly if you want, but the whole area really wears on Jack's sanity. Try to move out as quickly as possible.
Go down the steps into the next experimental area and realize what the dead cultist was talking about in his diary. This is the new volunteer. It seems like this weird Yithian machine is keeping him alive with his organs in separate containers. This is pretty much a mercy kill by any measure, right? Press the button in front of the volunteer cultist to fire a burst of energy and finish him off. That will free up the crystal that is powering the machine. We'll need that for the next step.
Pick up the green crystal from the stand and walk off through the metal door to the side. Go down into the next area with the large portal structures. It's sealed off with an alien door, but you can just press the panel to open it up. Note that you can't take this crystal, which is why you need the one from the first machine.
Walk up to the crystal stand on the right side and face the opening. Open up the inventory screen and select the crystal. This should put it into the slot and power up the machine. Walk over to the left side and press the big button to open the portal and have a bit of a third encounter. That should wrap up the prologue and set a lot of events in motion for poor Jack Walters. It can't be helped though.