In this guide I will explain how I got S rank on all the maps. The methods used may not be optimal but I'm not a super good player so if it worked for me, it should work for most people. Comments are welcome but I can't promise I will test suggestions, or change the guide.

The next list is the minimal requirement for an S rank. Instantly restart the mission when you fail on any of these points.

• Arrest all enemies alive.
  
• Secure all the civilians.
  
• Bag all the evidence.
  
• Complete all primary objectives (the points on the briefing screen)
  
• Complete all soft objectives (not listed in game)
  
• Do not get any minus points
  
• No officer can die.

To get the achievement Medal of Valor, play the game on Singleplayer, and then either Commander or Practice mode. Any S rank that is obtained in a Multiplayer game wil not count towards the achievement.
Never end the map by pressing Y. The game will end automaticly when all objectives are completed so if it does not take you to the end screen, you are not done yet.
Your teammate Bots are not smart. Give them small tasks and keep them behind you most of the time. Let them make arrests and secure evidence mainly or let them clear small rooms. Sending them ahead in bigger spaces will get them killed.
When trying to arrest an enemy, always shout commands at them(F by defaut). If you just shoot without talking they will not surrender as fast.
When a target is kneeling in a dangerous spot to arrest, use commands to let them crawl to you so you can arrest them without putting your team in danger. MMB on a kneeling target, Move>To my position. A captured civilian/enemy can get killed in the crossfire by an active shooter who is shooting at you so be carefull when they are in places like doorways etc.
If you dont get an S while you are sure you did everything correct, you have to do the math on the endscreen. Arresting a civilian/enemy will give 35 points so the total score on the endscreen for these groups should be the number arrested multiplied by 35. If it doesn't match a mistake was made and someone died. A dead suspect/civilian will give 5 points.

Primary weapon
There are 2 main options, the pepperball gun or beanbag shotgun. In most maps both are fine, but there are some pros/cons to both. Always put a flashlight on the primary weapons, since NVG cant be used because a gasmask is a must.

Pepperball gun
Good on shorter distance. Shoot 5-10 pepperballs in 1 spot to create a cloud of gas, this will make enemies stumble and cough for a few seconds. Still you need to spam F to make them comply. This can also control multiple enemies that are close to each other. It can function like a mini gas grenade if you use it well because you dont need to have direct contact for the pepperballs to have an effect on targets.
Enemies that are shot over any kind of distance react very badly to voice commands after being hit with pepperballs. In general you need to move in close with the commands for them to react, this can be dangerous. Mostly use pepperball in short/medium distances.
Pepperball uses a lot of ammo, its not rare for enemies to need half a magazine for them to finaly kneel down. Depending on the number of enemies on the map I used up to 7 magazines, but still got very low at the end of the mission.

Beanbag shotgun
Good on longer distance, enemies will react better to this than the pepperballs when they are far away.
Better agains enemies with gasmasks.
A headshot with a beanbag kills the enemy!!! This will ruin a few of your runs so be aware.
The shotgun has not much room for error since it has a pretty slow fire rate, so maybe 1 or 2 chances to hit the target before they will start shooting you.
Dont use a sight attachment, they make aiming weird over short distance and when leaning its also confusing in my opinion.
The beanbag shotgun uses a lot less ammo then the pepperball setup so much more room for other gear.

Secondary weapon
You can pick any pistol here. Only take max 1 magazine for it, or even no ammo, since you dont need it for killing. In some maps its useful to shoot out a few windows, so keep that in mind.

Armor
For most cases the standard light ceramic armor is fine. There are a few harder missions where you might die alot, in this case go for the heavy steel armor.

Grenades
In pretty much all cases use gas. Only a few maps will have enemies with gasmasks, in this case use flash, but gas is the default choice.

Long tactical (Back item)
Either the M320 Gas or the Shield work good for me, but the Mirrorgun also is a valid option, this also depends on the map, aswell as your own play style and prefference. Use the M320 gas mainly when you expect that you don't have enough throwable grenades for the job, aka big maps.

Tactical (Other equipment)
Carry 1 wedge to quickly block a door when I dont have time to make the bots do it, and the lock pick gun. Taser is an option for some maps but in general not very usefull. C2 can kill people behind the door so dont use that.

Head gear:
Gasmask is the only option.


Primary
Best option is to give all bots a beanbag shotgun. They dont understand how to use the pepperball rifle the right way so shotgun for all is the best. Also 1 hit with the shotgun stumbles the enemy, with pepperball it needs like 5, so way more likely the bots are effective with the shotty.

Secondary
Just pick any handgun for them, but DONT give them any handgun ammo!!!
In hectic situations the bots will switch to secondary and kill the enemy. This will ruin many runs so just dont give them any ammo for the handgun.

Armor
This might depend on your style of play but I normally take more damage than the bots so it was rare that they died and light ceramic armor has been fine on all maps. If your crew dies alot and ruins your runs upgrade the armor.

Grenades.
I choose to give them 2x Gas and 1x Flash, just so I can command both teams to clear rooms with any option that works for me at that moment.

Tactical (Other equipment)
Give the bots 2 wedges each. The rest is useless, C2 might kill so dont use that, they dont understand the lockpick gun so that wont do anything for bots, and pepperspray/taser will not be helpfull in any situation.

Long tactical (Back item)
On their backs I give each bot a different tool so they can be helpfull in many situations. I gave the 4 of them: Mirror gun / Shield / Breach Shotgun / M320 Gas

Head gear:
Gas mask is the best option.

In most maps there will be multiple routes you can choose to complete it, but often times there is one that is the safest/least exposed. Finding the right route is often the key to getting S rank.
If there are multiple spawn options for the map, I always took the top one so the guide is written from that perspective unless specified otherwise.
Its not a bad idea to complete all maps once with normal guns if you haven't done that already. This gives good insight in the map layout, and make it easier understand these descriptions. I expect most people who are going for S will have basic knowledge already, so this is not written for people who go in a map for the first time.
Some maps have traps, they spawn on different spots every time you reset so each door must be checked on those levels.
All the soft objectives are mentioned per mission, but not in much detail. For extra info and screenshots check out this Steam Guide:
https://steamproxy.net/sharedfiles/filedetails/?id=3113593191

I made a map only for Port Hokan so far to explain the route that worked best for me. I'm planning on making a few more of these for the harder maps, but it gets pretty ugly when there are multiple floors on a map.
For detailed blueprints of all maps check out this Steam guide. This is also the source for the map I made.
https://steamproxy.net/sharedfiles/filedetails/?id=3137562299

Enemies
Enemies differ in gear and agression mainly. They will be named strong or weak. Strong means rifles/smgs with body armor, and highly agressive/accurate. Weak means no armor, mainly handguns and shottys. Also weak reacts a lot slower and is less accurate.
There is a wider range than just 2 options but its enough for this guide, you will find out fast what their level is.
An estimate amount of enemies will also be given, this will slightly change each reset though so its just an indication.

Range
Distances on the map from where enemies can engage. Short/medium/long. This will mainly impact your primary weapon choice. For less lethal gameplay long range is harder because your weapons are less effective.

Primary
Just advice on the best primary for the job. Most maps are fine with any, but on some maps one of them may have a clear advantage.

Overal difficulty.
Just a grade based on my experience completing the map. Same grading as the ingame ranking, F is easy, A is hard, S made me want to delete the game.

Enemies: Weak / ±5 suspects
Range: Medium
Primary: Any
Overal difficulty: F

Move around the left side of the buidling and enter through the double doors. Jam the first 2 doors on the left and from then go through the building counter clockwise and clear it. Use gas in the larger spaces.
This is one of the easiest, should only take a few tries.

1 soft objective:
Wounded veteran near the couches in the dining area

Enemies: Weak mainly, a few strong ones in the streamers appartment / ±10 suspects
Range: Short
Primary: Pepperball slightly better, shotty also fine.
Overal difficulty: E

This is clearing out appartments so all short distance. Use gas.
At spawn go right through the gate up the stairs. Clear the crypto farm and jam the door to the inside stairways.
Go back to the stair and go up another level. Clear appartment and after that the stairways on all levels. Then go the the main targets appartment. This is always locked. Pick it and gas the rooms and secure all the targets. Shield can be used to look around corners where targets are to then gas/pepperball them.

3 soft objectives:
Crypto farm
Harddrive on next to streamers PC
Pictures next to the streamers bed

Enemies: Weak mainly with 1 or 2 strong ones / ±15 suspects
Range: Short
Primary: Pepperball slightly better, shotty also fine.
Overal difficulty: E

You need to clear two houses so short distances, gas/pepperball are very usefull to clear rooms/hallways.
At spawn go up the stairs and go right down the road to the house covered by the tent. Go along the right side of the house and enter halfway through the hole in the wall. Clear this floor, the next floor, and the attic. Then move across the walkway to the other house, clear the top floor and then the bottom. Go out the back into the garage and clear tunnels.

2 soft objectives:
Cash on a desk
The wounded child in the bed

Enemies: Strong / ±8 suspects
Range: Short with outside areas that are medium distance
Primary: Pepperball
Overal difficulty: D

This is a good one to use wedges. Go around the outside of the building and block most entrances, dont forget the roof. Then pick any entry point and clear the building. Use gas in the larger rooms, and just spray pepperballs in smaller rooms/hallways.

No soft objectives on this map.

Enemies: Strong / ±3 suspects
Range: short
Primary: Beanbag shotgun
Overal difficulty: D

TRAPS! Peek every door! Enemies use Gas masks so use FLASH on this map.
Move around the outside the house on the right side and walk up the stairs. Here you can enter the top floor from the back. Use flashbangs and use the shield to peek around corners. There will only be around 3 enemies but they are very agressive so be careful to not to get ambushed because they kill you fast.

1 soft objective:
Boxes with documents in the hallway

Enemies: Strong / ±10 suspects
Range: Short
Primary: Pepperball
Overal difficulty: B

TRAPS! Peek every door!
Again a good one for Wedges. I enter on the fire escape and once in the hallway go right. Wedge all the doors to the 4 bedrooms, and also 1 or 2 doors to the central area, then clear the hallways and central area and the few siderooms. Now all is clear exept the bedrooms.. The order is not very important but the room furthest on the right it the hardest to get in, use the room next to it to enter on a easier point. The others are no real issue just watch out for the windows/balcony.

No soft objectives on this map.

Enemies: Strong / ±12 suspects
Range: Short/Medium
Primary: Beanbag
Overal difficulty: A

This is one of the harder ones in the game. There are many weird places like server rooms where the enemies can shoot you while they barely see you. Also lots of windows they can shoot through once inside. They have strong weapons and are very accurate.
Go around the left side of the building and go in on the ground floor through the double doors. When inside Wedge the door in front and also the one left up the stairs. Then take your team to the right and clear the building counter clockwise, first downstairs then up, do the middle area's at the very last since this is the risky part so you wanna make sure everything around is cleaned up.
There is also a roof area where you can enter but the cover is not good on those points for non lethal. There can be enemies on the roof so you can also clear the roof first and wedge the doors.

No soft objectives on this map.

Enemies: weak / ±5 suspects
Range: short
Primary: pepperball
Overal difficulty: F

One of the easier maps. I go in at the beach and clear the house floor by floor. Throw gas up the stairs. This should only take a couple tries.

1 soft objective:
Bag with cash on the couch

Enemies: Strong / ±20 suspects
Range: Long
Primary: Beanbag shotgun
Overal difficulty: S

This one is rough, long distances with many places to hide for the enemies with nasty angles.
Go in through the front, clear the shop and the backrooms. Then move to the hallway, and clear the left loading area fast and go back to the hallway. Now open the left door to the warehouse. Restrain targets close to the door but ignore shots from across the hall. Go directly left up the stairs and clear the office. Go out of the office on the other side, and from the balcony controll the space below. Clear this area and check the office for the FISA agent and evidence.
That was the controllable part, now there are some options, depending on situation.
If it is to messy in the big sorting area, move back to spawn and move around the buidling, in whatever way seems to go right for you, or maybe even do both sides. With all the outside clear, try enter in either the back left or back right of the sorting area and clear it from there. Luck with the spawning locations of enemies is big in this one.

Its also possible to clear the entire outside first, because that is the easier part and its nice to have that taken care of before moving inside. But its a big map and very time consuming. On this one I died a lot so getting through the difficult parts early felt better then doing all the easy prep and then still die in the warehouse.

2 soft objectives:
A body in a pool of blood close to the FISA office
Weapons in a truck, outside back left.

Enemies: Strong / ±15 suspects
Range: Short/Medium
Primary: Both are fine.
Overal difficulty: C

Move in through the front doors and clear the top floor. wedge the door at the end of the hallway leading downstair(or go down the stair and wegde the door there) dont enter the lower floors through there, its horrible spot.
Now go back and exit through front door and go down the stairs on the side of the building. Enter the house here and clear the floor. When you made a full circle go down the stairs here, dont use the living room stairs.
Now clear the kitchen/theather room and then the living room, be careful because there are a lot of windows the enemy can shoot through from the oustide. Go back up to Amos office and go outside there. Clear garden and wedge the basement. Continue outside to clear the party/pool areas al the way around the house etc.
Then go down in the basement at the bar and clear basement. Use gas in these rooms.
In most cases Amos is in either the movie theater, basement or office.

2 soft objectives
Illegal material on the bed of the top floor left bedroom.
Illegal material in the basement creepy room.

Enemies: Strong / ±4 suspects
Range: medium
Primary: Beanbag
Overal difficulty: D

This is a weird one. All others are based on tactics, this is just a speedrun.
It took me a while to find out that the enemies will start killing civilians after only 120 seconds, and as soon as civilians are dead, you wont get an S.
So basicly just sprint inside through the front door, pray you find and control all the enemies within 2 minutes and after that clear the bombs/civilians.
If you dont manage to get it in time you will hear a gunshot in the distance, from an enemy somewhere in the building killing a civilian, and that is your sign to hit the restart.

No soft objectives on this map.

Enemies: Weak / ±12 suspects
Range: Short/medium
Primary: Pepperball
Overal difficulty: E

Nothing special here, make sure you clear all the houses in the beginning before going down in the tunnels. Once in the tunnels use gas and pepperballs to clear it out. Dont go to fast and it should be done in only a few tries

2 soft objectives:
Passports on the table. in a house above grount
A raft deep in the tunnels

Enemies: Strong / ±10 suspects
Range: Short
Primary: Pepperball
Overal difficulty: C

Its a bit dark and you have to know the map well, but after that its not to bad.
Go in the fire escape, down the stairs to the upper floor entry point. When inside wedge the first door on your left. Now go to the right and wedge the door at the end off the hall to the gallery. Clear the other 2 rooms on this little hallway. Then move the other direction and clear the hallways and big room on the left, and the second big room behind it with the balcony. Stay away from the edge, just arrest and clear dont shoot down.
Now move back in the hallway and go down the stairs in the middle. Clear the room and go out on the far right and go in the butler passage (check map). Clear this hallway and wedge of the exits, and move back the way you came to clear the rest of the floor room by room.

No soft objectives on this map.

Enemies: Strong / ±15 suspects
Range: medium
Primary: Beanbag shotgun
Overal difficulty: A

This map is pretty big with agressive enemies. There are also guys with bomb vests who will rush you and blow up. These guys dont care much about pepperballs, for this reason the shotty is advised for this map. Also gas them to keep them busy while you try to get them to kneel down. The taser might also come in handy on them.

When you enter the building, move in to the first area Wedge the double door to the dancefloor, and move on left through the coat room. Then in the staff area Wedge the other double door to the dancefloor and prepare to move through the single door into the club. Clear this area, do not go up the stairs here. Continue to the two double doors, wedge the right one to the bar and continue through the left to the bath house, gas it up and clear this whole area including the bathrooms/storage rooms. Dont go on the dancefloor yet. Move back to the stairs in the corner of the bath house and go up here. Shoot some windows out with the pistol to check the other side. Move along and clear the top floor counter clockwise. There are some nasty angles they can get you from but dont rush and circle around the whole floor arresting all. When you did a full round you are back where you started, go down the straight stairs in this area, where on the right you have the dancefloor and straight on a bathroom. Gas the dancefloor and clear, big chance the target enemy is here, then do the bathrooms and all should be clear.

No soft objectives on this map.

Enemies: Mix of weak and stronger ones, not super strong / ±18 suspects
Range: medium long
Primary: Beanbag shotgun
Overal difficulty: B

Pretty big map with a lot of open spaces. Beanbag works best for this. The enemies dont have great armor and and are not the most aggressive, but have decent guns and accuracy.

Move straight ahead around the truck, then go in the main building on the side. Clear this first area and then move in the offices from the small door on the right where you came in, move through that room to the stairs. Clear the upper layer then go down again into the showrooms/sales area's and clear the rest of the main building. Now go outside and go clockwise to clear the outside and then into the garage buildings and keep clearing all the way around.

2 soft objectives:
Documents in the office next to the showroom
Report 1 of 3 possible illegal activities in the garage: Cash, weapons or drugs. When 1 of them is reported the other 2 will not be possible to report but it will count for the objective so no worries.

Enemies: Weak / ±15 suspects
Range: Shot/Medium
Primary: Pepperball but both is fine
Overal difficulty: D

Decent sized map with some tricky spots but not to bad. Enemies are pretty easy, but some have decent guns. Lots of small rooms and hallways so the pepperballs gas cloud is usefull here. Outside some medium range but not very difficult.
The two targets who need to be arrested wear red sweaters, they are a bit more agressive.

Move in the house on the left at the garage and clear the first rooms, then keep going and move counterclockwise along the inside of the house. Clear the inside of the house as good as possible. The house is like a U shape with a courtyard in the middle, this courtyard is the most dangerous so clear the house all around it before you go in there. There are also some tunnels which you can reach from the inside also, so do them while clearing the inside. When inside, tunnels and courtyard is clear move around the outside to make sure its all cleared and then take the path to the church building. When you checked that area the whole map should be done.

1 soft objective:
planning board in the bedroom

Enemies: Strong / ±15 suspects
Range: Short
Primary: Both
Overal difficulty: C

Big map with 5 floors but not very difficult spaces. Make sure each floor is fully checked before going to the next, there are many civilians and you dont want to walk all the way back through the map to find the last one so get them all on the first passing.

Choose the parking entrance. Move to the left of the building and go in there, and go to the left, clear a room and hallway then go into a single door to the middle rooms of this floor. Then clear the middle rooms before moving to the reception and go counterclockwise around the floor to the patient areas and clear that. Then time to move up, dont use the main stairway, but the small one between 2 bathrooms. Go all the way up, and enter the floor, clear it clockwise and defuse the bomb. Then go across the walkway, take the second door and clear the floor and take care of the second bomb. Then go down the small stairway on the opposite side of the floor from where you enterend. This floor should have the target enemy. Clear it either way around, make sure to also get the middle rooms. Now go down to the last/bottom floor and clear that. This floor is pretty big so much rooms to check but most times the enemies are in the beginning.

No soft objectives on this map.

Enemies: Strong / ± 20 suspects
Range: Long
Primary: Beanbag shotgun
Overal difficulty: S+

This is the hardest map if you ask me. It is dark, with large open spaces and agressive enemies with good guns. The spawns are also important here, if multiple enemies spawn in an open space it's very hard to control. Pepperball is useless because of the distance and number of enemies, so beanbag is the way to go. When they are kneeling, use commands to make targets come to you when they are in exposed positions.

From the start follow the path and clear the first area and check the container for soft objective. Take the left passage en move along to check the left and go right. Don't move out into the open yet. Keep going through the containers making sure all is clear, there are 2 more possible evidence containers along this way, and move to the small building in the corner of the map. When that is checked move in the direction of the main warehouse, crossing the big open area on the far right. Make your team clear the "control tower" building on both floors, wedge on the second floor door to warehouse. Go outside again and move along the building, and wedge the single door to warehouse. Keep going along the building crossing the open space to the other side of the map, clearing the small office buildings. Move around the left side of the warehouse and enter it here. Best option is to clear it clockwise but both directions are fine, going in the hidden area and pop out the container on the others side, keep going around the building untill the whole warehouse is done.

5 soft objectives:
Container with evidence 1
Container with evidence 2
Container with missing people (always the same spot)
Close the container with missing people after reporting it.
The laptops in the creepy area in the back of the warehouse.

If you have tried this mission many time like me, save the container with missing people for when you have the entire map cleared to spare you the dialogue because you dont want to hear that each run.

Since this map is pretty complex i made a map for it explaining the route. The green dots are Doorjams.