This guide was adapted from the guide written by Halfgild Wynac which was translated by The LxR.
All credit goes to them. Thank you for your fantastic work.
Please refer to the map created by Halfgild Wynac.
I have tried to keep the guide short, so I have not included exact directions to NPC houses.
It took me 18 hours to finish Clara's scenario.

13ventrm's general guide to daily survival is really essential reading, so please read that!
When you are doing quests you generally want to befriend the NPC you are talking to. Being rude usually results in quests failing. One of the major themes of this game is manipulation. The NPCs will lie and manipulate you, so do the same to them. Play everyone off against each other so you can buy enough bread to get through the day. That being said, it is very easy to mess up quests by choosing the wrong dialog options, so save before you talk to NPCs.

Shmowders are arguably the most important item in the game. You will want to hoard as many as you can for the last day. On the other hand, I did not find medicine very important. Reloading a save is probably a better option if you get hit by a cloud or a rat. I never bothered looting houses either, because you get so much money and items from doing quests.

It is necessary to understand certain terms in order to fully understand the story in this game. I have also written a mini encyclopedia (with spoiler tags). So please consult that if you are confused about who is who and what is what.

Controls
I – opens inventory
Q – opens Quest menu
P – opens player statistics
L –opens letter menu.
When you see a sigil on the bottom left of the screen you probably received a letter or got a quest update, so check the appropriate screen.

Trading
When trading with an NPC, click the item you want (on the left) and then click the item you will give them (on the right). You can choose multiple items. Then click the V button at the top right. If you want to cancel, click the X button on the top right.

When fighting you want to swing before you move forward because the animations are a bit slow.

Food
Nuts -1% (save them for trading with kids)
Crackers/biscuits -2%
Dried Fish -7%
Eggs – 12%
Canned Vegetables -12%
Milk -7%
Smoked meat – 17%
Dried Meat – 17%
Loaf of Bread – 25%
Fresh meat – 25%
Fresh fish – 25%
Lemons increase hungry by 10 but increase immunity.

Clara can only use the scalpel and the pistol.
But she also has a long distance hand attack
You need to hold your crosshair on the target the entire time the animation is playing.
You can cure infected citizens with your hands at the expense of your own health.
Your reputation will constantly be falling.
It will take 1 and a half days for it to go from 100 to 0.
It will not fall when you sleep.
So it is sometimes better to just sleep rather than wander aimlessly.
There is a Steam Achievement for seeing every play. If you want to get this achievement sleeping at Older Vlad's house is a good idea.

This map shows the shops and character locations.

You wake up at the cemetery.

Main Quest - The Harbinger
Talk to the masks and Katerina inside the lodge.
Go and meet Alexander.
Go to the rocks near the railway station.
You will find two people there.
Talk to the dog head.
Try to heal him with your hands.
Talk to the man nearby.
Talk to Grace.
Go to talk to the Haruspex in his hideout in the Works district.
He will be in the 4th building, south of the railroad.
Go to Anna's house.
Cure the wounded person.
Talk to the Bachelor.
Talk to Alexander for a reputation boost.
Try and buy some food now.

Quest - For those with the freedom of choice
Talk to Anna
Talk to Notkin to get a gun.
Talk to Anna to get 1500 coins.

Quest - The Hooks (truth revealing itself)
Talk to Alexander after you finish the main quest.
Talk to Katerina about Georgiy.
Talk to Georgiy
Talk to Maria.
Talk to Georigy, say "Geogiy, Georigy..."
Talk to Alexander to get reputation as a reward.

There are bandits behind the train station if you still need a reputation boost.

Main Quest – Spirit of the restless Kin
Talk to Alexander
Talk to Younger Vlad.
Talk to Older Vlad.
If you say the right things he will give you 2500 coins.
Talk to Aspity
Visit the Haruspex at his hide out in the factory district.
Talk to Aspity.
Be careful what you say or you will fail the quest.
Tell Alexander she is innocent or she will soon fall ill.
(You will take a reputation hit thanks to your sister)

Quest – Grace
Talk to Katerina.
Talk to Lara. (optional)
Bring Grace bread, milk and a flower.
You can find flowers on the steppe.
If you convince Grace you will gain 10 reputation when you talk to Katerina.
(don't bother with this quest, save the bread)

Quest - The Curative Substances
Talk to Younger Vlad.
Talk to Anna but don’t take the medicine.
Talk to the herb gatherers near the cemetery.
Talk to Andrey.
You can now take the five tablets from Anna.
If you give him Anna’s medicine you will get 500 coins.

Quest – The Living
Talk to Lara.
Use a lock-pick to open the house Lara tells you about.
Talk to The Harpist and talk to the Bachelor too.
Lara will give you 2000 coins or 5 reputation if you refuse.

Main Quest - Seeds of the caravan
Talk to Alexander
Talk to Anna.
Talk to Capella.
Talk to Anna.
Talk to Alexander.
Tell Alexander Anna is innocent or she will get ill.
(You will lose reputation for protecting Anna from justice)

Quest - Eve
Talk to Katerina.
Talk to Yulia.
If you tell Yulia she is wrong you will get 30 reputation but the quest will end.
If you agree with Yulia it will continue.
Talk to Eve and convince her.
Talk to Katerina for 1000 coins and 10 reputation.

Quest – Who will injure the Bachelor?
Talk to Anna.
Talk to Eve
Talk to Rubin in his laboratory near Bad Grief.
If you promise not to tell the Kains he will give you two black vaccines.
(Talking to the other Kains will reduce your reputation.)

Quest – Who will sting the Haruspex?
Talk to Capella.
Go to the house and talk to the Bachelor.
Idler is standing outside near the entrance of this area of houses
Take the powder from Idler.
The Haruspex is hiding in the house opposite from where Idler was.
He will give you immune mixtures if you help him.
If you tell the Bachelor about the Haruspex you will get 2000 and neomycin.
If you tell Capella that you hope the Bachelor will test the medicine you will get 5 reputation.

Main Quest – Robbers and cutthroats.
Talk to Alexander.
Talk to Bad Grief.
Talk to Notkin.
Talk to Bad Grief.
Sneak into the warehouse.
Talk to Barley inside, tell him to look in the corner.
Go back to the door you came in and jump onto the box next to it (It is possible!)
You are safe up here.
Take the bag to Alexander.
Talk to Bad Grief (save!)
Say "Filin Filin..." to get the answers you need
If you don’t tell Alexander that Bad Grief is innocent he will get sick.
You will lose reputation for protecting Grief.

Quest – The Puppeteer
Talk to Katerina.
Talk to the masks at the theatre.
Go to Maria’s house and save before talking to her.
If you give them 500 coins you will get 10 reputation (not worth it.)
If you say you got the wrong door you will lose 10 reputation.
If you say you hate her you will lose 30 reputation.
If you say you are no saint you will gain 10 reputation.
But if you are then rude you will lose 30 reputation.
Talk to Mark.
Talk to the masks at the theatre.
Talk to the creature standing on the stage in the theatre.
Talk to Katerina if you tell her about the creature you will get 10 reputation.

Quest – Round up
Read Lara’s letter.
Talk to Alexander.
Find the Haruspex in the infected district.
He is on the ground floor of the building opposite factory building 1.
Its the building to the right of the white hand on your map.
If you warn him, Lara will give you etorphine and 2 bits of smoked meat.
If you trick tell Alexander where he is, he will give you 500 coins and 10 reputation.

You can enter the rat races today.
Tomorrow will be hard so stock up on food and medicine today.
Try to get 3 pieces of fresh meat for the main quest asap

Main Quest – Rubin's Communion
Talk to Alexander
Talk to Younger Vlad.
Bring Rubin 3 piece of fresh meat and 3 bottles of Twyrine.
Talk to Georgiy.
Talk to Rubin again.
Talk to Alexander to get 10 reputation.

Quest- The Twins.
Read Katerina’s letter.
Talk to Peter.
Talk to the man in the far corner of the pub
Talk to Alexander.
Go back to the pub and talk to Andrey.
Talk to Peter.
If you tell him the truth he will give you 5 bottles of Twyrine.
If you tell Katerina the result you will lose 2 reputation.

Quest – The Cathedral
Talk to Capella
Talk to Maria.
If you say you are scared to go she will give you 4000.
Talk to the Bachelor at Eve’s house. (optional)
Collect 20 bottles of water (!!!).
Give them to the guards to enter the Cathedral.
Talk to Capella.
If you tell her Maria nearly killed you, she will give you 4000 coins.
If you ask her to put in a good word for you, you will get 10 reputation.
If say it wasn’t that bad at Maria’s you will get 5000 coins and 2 reputation.

Quest – Best Friend.
Talk to Grace
Go to Raga Barrow behind the cemetery in the evening.
Get ready for a fight, they drop good loot!
At 9pm Grace’s friend will be at the top of the borrow.
If you DON’T say “Of course, I know.” he will tell you a lot.

You need to find your sister everyday from now on, or she will permanently infect districts. Sleep for at least 4 hours in order to get a letter from your sister. She always hides in a house in plain sight. After you find her a group of supporters will appear that you will also need to find each day for the same reason. To make them disperse, you should show them in a positive way that you are the real Clara.

Your reputation will also constantly be falling today, at various speeds, so be more careful than usual.

Main Quest – Angel of Death
Read Alexander’s letter in the evening.
Talk to Eve (optional)
Talk to Yulia.
Your reputation will start falling quickly now.
Do not talk to Eve as she will take most of your items away.
You need to find the Bachelor.
Depending on the time he will be in a different place.
From 2pm – 4pm – At Lara’s house.
From 4pm – 6pm – At Aspity’s house.
From 6pm – At Eve’s house.
After you talk to him you will not be allowed to leave the house.
So do your other quests first.

Quest – Little Sister
She is upstairs in a building next to the Cathedral garden.
You will get a Steam Achievement.
Read the Albino’s letter
Talk to Grace.
Talk to the Albino at the barrow at 9pm.
(there is no reward but the enemies in the area may have good loot)

Quest – Charon
Talk to Katerina
Talk to Capella.
Try to give Younger Vlad the book.
Talk to Katerina. (There is no reward)

The Inquisitor arrives today, she will be in the Cathedral.
From now on, if you tell her about clean districts (after finding your sister and her supporters) she will give you 2000 coins each time.

Main Quest – Vengence.
Talk to the Bachelor to get 1000 coins.
Talk to the masks in front of the cathedral.
Find the coat and mask in the cemetery by the pile of bodies..
You can enter the Cathedral after 12.
For now talk to Alexander.
Talk to the Bachelor in the theatre.
He will give you another quest. (see below)
If you give him the mask he will tell you about the Inquisitor / The Powers That Be.
Go and talk the Haruspex in the short block of the Termitary.
He will give you another quest. (See below)
If you give him the coat of the outcast he will tell you about the Inquisitor.
Talk to Alexander.
Talk to Katerina.
Talk to Maria.
Talk to Capella.
Talk to Katerina.
Go to the Cathedral.
If you find them guilty you will lose 50 reputation and they will fall ill.
If you find them innocent you will gain 50 reputation and they will live.

Quest – The Bachelor will sow a seed of malice
Talk to the Haruspex. (see above)
Talk to the family.
If you lie and keep the Twyrine, you will lose 5 reputation.
If you give it to them the Haruspex will give you 2000 coins.

Quest – The Haruspex will sow a seed of malice.
Talk to the Bachelor (see above)
If you go and give the creature the weapon, you will get 10 stems of white whip.
Talk to the Bachelor again.
He will give you 5000 coins or 5 reputation if you refuse the money.

Quest – Little Sister
Sleep for at least 4 hours to get her letter.
She will be hiding in the house next to where Younger Vlad lives.
Her supporters will appear in the courtyard north of the Boiler.

From today you can tell the Haruspex or the Bachelor where your sister is after finding her. The Bachelor will give you 4000 coins and the Haruspex a Panacea. However doing so will reduce your reputation by 30.

The army will appear tomorrow, so try to improve your reputation or cure any infection you might have today.

Main Quest – The Town ; it's entrails.
Talk to the Inquisitor
Go to the long block of the Termitary, on the third floor.
Talk to Taya.
Talk to Sticky.
Talk to Taya and choose the third reply.
Enter the Abattoir.
Talk to the elder.
Talk to Aspity.
Talk to the Elder.
Talk to the Inquisitor.

Quest - Little Sister.
Sleep for 4 hours to get her letter.
Go to the building that overlooks the fighting ring near the Abattoir.
Her supporters appear behind Lara’s house.

Quest - Tracking down the Bachelor
Read Maria’s letter.
Go to the house next to the town council and talk to the Bachelor.
He is being protected so be careful.
If you help the Bachelor, Maria will give you 2000 coins, feromicine and 5 reputations.
If you tell the Haruspex where the Bachelor is he will give you 3000 coins and you will lose 5 reputation.

Quest - Tracking down the Haruspex
Read the Inquisitor’s letter.
You can find the Haruspex in a "doube house" next to Sticky’s place.
He is being protected so be careful.
If you help the Haruspex and tell the Inquisitor she will give you 1000 coins, monomicine and 5 reputation (don’t tell her you don’t need a reward!).
If you tell the Bachelor where he is, the Bachelor will give you 5 tablets and you will lose 5 reputation.

Main Quest – The Town; it's Head
Talk to the Inquisitor.
Talk to Georgiy.
He will give you 5 tablets, 5 revolver bullets and a cape repellent.
Go to the short block of the Termitery.
Talk to the Bachelor on the first floor. (optional)
Talk to the Haruspex on the top floor.
Talk to Georgiy.
Talk to Victor.
Climb the Polyhedron and talk to talk Khan.
Say "Fains I"
Step on the drawing at the bottom.
Talk to the people inside.
Go back to the Cathedral.
Talk to Block at the Town Council.

Quest – Little Sister
Sleep for at least 4 hours to get a letter.
Your sister will be in a house overlooking the “stairway to the sky” near to Lara’s house.
Of the three house to the south of the stairway, she is in the middle one.
She is on the ground floor on the left side of the building.
Her supporters will appear near Isidor’s house.

Quest – Tracking down the Haruspex
After finishing the main quest you will shortly get a letter.
The Haruspex will be in a building near the Olgimskiy’s house.
He will be guarded.
If you help him you will get 5 reputation, 2000 coins and monomicine from the Inquisitor.
If you tell the Bachelor where he is, you will get 5 tablets and lose 5 reputation.

Quest – Tracking down the Bachelor.
After finishing the main quest you will shortly get a letter.
The Bachelor is in a house next to the pub.
He is guarded.
If you tell Maria she will give you morphine, neomicine and 3000 coins.

Main Quest – Simon
Talk to Notkin.
Talk to the Bachelor at Rubin’s lab.
Talk to Maria.
Talk to the soldiers at the town council.
Talk to Blok.
Enter the town council. (be careful of infection).
Talk to the man inside.
Talk to Blok.
Talk to the man outside.
Go to Factory Building 3.
Talk to the Haruspex there.
Talk to the creature behind the theatre.
Enter the tunnels. (Be ready for a fight)
You can glitch onto their heads and kill them unharmed.
Talk to Rubin.

Quest – Little Sister
Sleep for at least 4 hours to get a letter.
She will be a house overlooking the bone pillar
A soldier and disinfectionist are standing right outside it.
Her supporters are north of the park near Younger Vlad's hideout.

Quest – On traces of the Bachelor
After you finish the main quest you will get a letter.
The Bachelor is in a house overlooking the park south of the theatre.
He is guarded.
If you tell Maria she will give you 4000 coins and feromicine.
Or you can tell the Haruspex for money a reputation loss.

Quest – On the traces of the Haruspex
After you finish the main quest you will get a letter.
He is in a house close to Anna’s house, opposite a shop.
If you tell the Bachelor he will give you 5 tablets and you will lose 5 reputation.
If you tell the Inquisitor she will give you 4000 coins, monomicine and fermoicine.

This is the last real day so buy food and try and find a girl who will trade you Shmowders for tomorrow.

Main Quest – The Bound
Talk to the Inquisitor
Talk to Block at the Town Council.
Go to the weapon.
Talk to the soldiers near the wagon.
Heal the officer.
Watch the cutscene.
Talk to the officer again.
Go to Peter’s house.
Talk to Peter, Andrey and the Bachelor.
Go and talk to the Haruspex at his hideout in the factory district.
Convince him not to fight.
Go to the Abattoir and talk to Oyun.
Talk to the Haruspex there too.
Don’t tell him the town disgusts you.
Talk to the Inquisitor.
Talk to Block.
Now you need to talk to 6 of your Adherents (aside from Oyun)
(I hope you enjoy walking!)
You need to choose 6 volunteers.
After you have chosen talk to Block.

Quest – Little Sister
Sleep for at least 4 hours.
Your sister will be in a small house south of the Town council between two long houses.
Her supporters will be in a courtyard to the east of Lara’s house.

Quest – Tracking down the Bachelor.
Read Block’s letter.
The Bachelor is in the graveyard behind the Kain’s houses.
If you tell the Inquisitor she will give you 4000 coins, feromicine and 5 tablets.

Quest – Tracking down the Haruspex
Read the Inquisitor’s letter.
The Haruspex is in a house near Aspity’s place, to the north west.
If you tell Block he will give you 5000 coins and 5 tablets.

Read Aglaja's letter.
The last day. Well done for making it this far.

Visit the last theatre performance before 7:00 in the morning.
The Theatre will be closed later.

The Bachelor and The Haruspex will ask you to heal their Adherents.
If you have enough panacea and powders – do so, but don’t forget about your own Adherents.
If you heal their Adherents they will also come to the meeting.

Here are the lists of Adherents:
The Utopians: Eve, Georgiy, Victor, Andrey, Peter, Mark, Maria, Younger Vlad.
The Termits: Khan, Capella, Murky, Notkin, Sticky, Grace, Taya.
The Humbles: Lara, Yulia, Bad Grief, Rubin, Alexander, Katerina, Anna, Aspity and Oyun.

If you cure at least two groups of Adherents a letter from the Authorities will arrive.
Step on the drawing inside the inner chamber. Talk to everyone inside.

Quest - Final Proceedings
This quest will automatically start at 7pm at the Cathedral if:
You completed all the daily quests.
None of your Adherents are dead or infected

Talk to everyone and then tell Blok your decision.......