You have to collect the spirits in one run. If you miss one, you have to complete the entire game from the start.
To check the direction (or if you are missing a spirit) you can select the skill "Spiritual Connection" to see spirits in wolf form.

For the stories, you too have to collect 30 in one run.
For "State Washington's Forest" you can collect the stories during the second and third visits, too.
By the end of "Endron's Dam" you should have collected enough stories for the achievement. You'll find others during the rest of the game, so don't worry if you are missing a few.

Thanks to [AVBG] for some corrections.
I have to add, that some screenshots are no longer available. I don't know why.

Not missable: After you checked out the explosives you discover silver bullets. That sheet counts for STORY_001.
After you followed the mission tracker and eventually escalated the first time, you switch into Lupus form and cross the vent. After there you find a room with a plant on it. That's SPIRIT_001 you can absorb.
Follow the mission tracker downstairs and come into a room with two plants (SPIRIT_002, SPIRIT_003).
Continue till you encounter some scientists. Between the room down there and the previous "large" room there is a short hallway. Here you find the next plant(SPIRIT_004). Now look behind you, you find some mushrooms (SPIRIT_005).

After the Cutscene and the dialog with Rodko, as soon you can control Cahal again:
Turn around and go to the section with the wounded guy. Left on the Table STORY_002. Go ahead to the cable reel and you find STORY_003.

Go follow the way up to the next room. That's kind of a storage room. On two shelves you can find STORY_004 and STORY_005. In the same room on a metal and wooden chest you find STORY_006 and STORY_007.

In the storage room you can find two stone buddies. Look into the spirit world to get SPIRIT_006.
Turn around, go back and upstairs and then enter the room to you right. On the metal chest you can find STORY_007. On the right side of the same room you can collect STORY_009.

Follow the quest marker downstairs and you'll see a shimmering tree on your right side (SPIRIT_007).

Follow the path in a straith line and enter another storage like room. On the left and right side you can find story STORY_010 and STORY_011.

Follow the quest marker till you see two yellow clothed activists. At the right side you look upwards and you see a shimmering plant (SPIRIT_008).
Again, follow the quest marker till you find the next two yellow clothed activists. This time, the shimmering plant (SPIRIT_009) is on their left side. If you just go ahead you see STORY_012 on a wooden crate.
If you follow that path downwards, you eventually see a grave. Jump down there and read STORY_013.

Go back to the activists, follow the stairs to your right. STORY_014 is on the left side - again on a wooden crate.


Go back downstairs. Behind the quest marker you find and empty cable reel. There is STORY_015.

Follow the quest till Yfen opens a root blocked way for you. A few meters ahead on the right side you can jump upwards to the solar panels. Behind them you can find STORY_016.

Follow the quest marker and almost at the end you can see a shimmering plant on the right side: SPIRIT_010.

After you got access to the training facility (one way or another) you can find another shimmering plant (SPIRIT_011) on the right side of the inner yard behind some boxes.

After the level starts, turn left behind the building machine you find SPIRIT_012.

Follow the quest marker and keep your eye to the right side. Bevor the gate in front of the yellow control cabinet you find a plant (SPIRIT_013).

Go on and follow the questmarker. After you went upstairs you enter a control room. In the left corner you can find STORY_017.
Go further and you enter a kind of showroom. In the right corner you find SPIRIT_014.
Immediately after you enter the next greater enlightened room, turn left an walk along the wall for SPIRIT_015, SPIRIT_016 and SPIRIT_017.

Follow the quest marker and you come along STORY_018.

After the fight with the Exo, as you get nearer to the tank, you find SPIRIT_018 in the office room.
A floor below you find STORY_019.

After you placed the explosives, contrary to the waypoint, enter the ventilation shaft, go upstairs to a control room, where you can find stone buddies SPIRIT_019.

Go along with the story till you enter another control room. Besides the waypoint you find SPIRIT_020 and SPIRT_021. At the other side you can collect STORY_020.

Next you enter some kind of storage room, where you can absort SPIRIT_022 and read STORY_021.
Now DON'T follow the quest marker but turn into the left room instead. SPIRIT_023 is waiting for you. In the next room on the right side you can absorb SPIRIT_024.

At the lab, on the computer side, you can absorb SPIRIT_025.
When you follow the questmarker, BEFORE you go upstairs, go behind and collect SPIRIT_026 at the mushrooms.
AFTER you went upstairs, enter the room to your left for SPIRIT_027.

Go along till you are in the vents. When you jump down the yellow pipes you can find SPIRIT_028. Follow the yellow pipes and - before you cross the rotor - you'll find SPIRIT_029. AFTER you cross the rotor, turn left and at the mushrooms you can absorb SPIRIT_030.

Leave the Endron site and go to your Cairn. Follow the quest and after you spoke with Rodko you eventually come along a shimmering stone, which holds SPIRIT_031.
At the next parting of the ways: turn right and you can see a shimmering tree (SPIRIT_032). Turn left and follow the path. At the right side you can see two stone buddies (SPIRIT_033).
Follow the path and you see the Endron facility. Go near the cliff and turn right. At one of the jugs you find SPIRIT_034.

Jump back and face the facility again. Now turn left. After a while, at a bend to the right, you can see a bunch of fireflies. Turn Cahal towards them and you can see a glowing stone where you an absorb SPIRIT_035.
Go back and follow the path till you come across the street. At this point turn left and ignore the quest marker. Near the first building on the right side you see a trunk, where you can absorb SPIRIT_036. Go back to the street and turn right (again opposite to the quest marker) till you enter the construction site. Near the flood light at the cliff you can find SPIRIT_037.

Turn back, cross the street and follow the trail upwards. At the first possibility turn right and then left. When you see an opportunity to jump a few stone jumps upwards, look at the bottom left before you do that. That's SPIRIT_038.
Ignore the stone jugs and take the path to your right. Follow that path till you see another trunk (SPIRIT_039). Go ahead to the cliff and look left. There you can see another (greater) trunk with SPIRIT_040.

NOW you can follow the quest marker - at least till you talked with Declan. In the facility - in a fenced of area you find SPIRIT_041 and SPIRIT_042. You need to enter the facility and open the door in the control room upstairs.

After you control Cahal, turn around and look up. The shimmering plant holds SPIRIT_043.
After the next room follow the stairs downwards. Once reached the ground, turn right and follow the way to the end for SPIRIT_044.
Bevore you enter the elevator, enter the building via the vent on the right. At the center of that room you can collect STORY_023.

Use the elevator and follow the main quest. At the outer yard at the right side of the fence you find another plant for SPIRIT_045.
Turn back to the sidequest, and follow the respective quest marker to the end of the floor before you enter the room to your right. Roam through the vent and you find SPIRIT_046 in the office room behind.
Leave the room and follow the secondary quest marker to the control room for STORY_024 and STORY_025. Continue and enter the room with Victoria and the scientist for SPIRIT_047.

Follow the quest marker(s). After Cahal says, that he is inside, look into the room to your right. At the floor you find a toolbox for SPIRIT_048. Continue the quest till you encounter the entry to the next room. On the couch you find a notebook for STORY_026. Leave the room and continue to the server room. In a niche at the left side you can read STORY_027 and at a niche to your right you can absorb SPIRIT_049.

In the previous room you can cross into the vents on the (when leaving the server room) left side. Continue your way to the right. At the bulletin board you can read STORY_028 and absorb SPIRIT_050. Continue that hallway downstairs to the next bulletin board for STORY_029. Continue further downwards. At the ground level enter the door at the left side for STORY_030 at the couch. Behind the door to your right side (following the quest marker) you find SPIRIT_051.

At SPIRIT_051 turn around and enter the next server room. A 180° turn (right) for STORY_031 and a 180° turn (left) for STORY_032 and SPIRIT_052.

Follow the quest marker and at the end of the next hall you can enter a room to your left for SPIRIT_053. Continue with your quest and follow the quest marker till you come to a room with a large "A2" at the wall. After the room look left and you can see a plant (SPIRIT_054) next to a bookshelf. Turn around and follow the floor to the end for SPIRIT_055 and SPIRIT_056.

Now keep following the quest marker till you go outside. In the "plant boxes" you find SPIRIT_057 and SPIRIT_058.
Still outside at the wall near a heap of stones you find a plant (SPIRIT_059). Follow the quest marker and you come across SPIRIT_060 in form of another plant on the ground.

The last plant (SPIRIT_061) for this level you can find in the next area (parking lot) at the right side to the left of the pedestal.

Follow the quest till you can open the door and the ventilation shaft. Enter that ventilation shaft and follow it till you reach the roof. At the roof are two plants: SPIRIT_062 and SPIRIT_063.

At the start of the level: next to the white pickup you'll find SPIRIT_064.
In the building, before you enter the elevator, look to your right and you see SPIRIT_065.

Follow the quest marker, use the elevator and when you enter courtyard, turn right for a plant and SPIRIT_066.

Before you hack the computer, go to the left table and investigate the stony buddy for SPIRIT_067.

Again, after you leave the elevator and enter the open area, go strictly straight and you can see a plant (SPIRIT_068). In the same area at the oppsite you find another plant (SPIRIT_069).

After you've unlocked the doors, leave the courtyard near SPIRIT_068. You see a large chasm, use the way with the pylons and you find a bush with (SPIRIT_070).
Continue that way, jump upwards, cross the vent and after you leave the vent you can open a cell, where (SPIRIT_071) is locked up.
Continue your way. In the same room where you can hack the terminal you find (SPIRIT_072).

Go back to the courtyard and follow the remaining questmarker.
Right to some yellow stairs you find your next plant for (SPIRIT_073).

You can open a gate, where a elevator for crates and stuff is behind, so you can follow the quest marker. At the opposite side of the upper room (when you entered) , you find a room where you can cross the fence as wolf. Behind this fence are two stone buddies (SPIRIT_074).

Follow the quest marker. After the reception turn left to a fitting room. The plant (SPIRIT_075) is placed obviously. Now go back and follow the hallway to a devastated office. Next to a fallen over cupboard you find (SPIRIT_076). In the same room is a notebook, where you can read another STORY.

After you killed Rodko, follow the questmarker upwards to the pipes. Now turn right and you'll see some shimmering mushrooms (SPIRIT_077).

When you left the vents, slightly turn left for (SPIRIT_078).

After the helicopter scene, turn Cahal to the right and follow the wall for another bunch of mushrooms (SPIRIT_079).

Pass the two guards to your right and go to the basketball field. In the outer ring you find some mushrooms (SPIRIT_080, SPIRIT_081).

Back in the mess hall, after you talked with Schibetta, continue to the upper floor. At the opposite side, two ventilation shafts are now accessable.
The vent from the stairs to the right side: leaving the vent into a cell you find (SPIRIT_082).
The vent from the stairs to the left side (don't go right / upwards): after leaving the vent into another cell, you find mushrooms at the wall (SPIRIT_083) - in addition you can find another STORY.

In the workshop you can cross a vent to access an office. The plant in the middle desks holds SPIRIT_084 and in the corner under a board you can find SPIRIT_085.

Cross the vent and you are back in the mess hall. Hold on the right side (in direction to Eric Ross) and you find another ventilation shaft. You can see Eric Ross, but can't access him from here. Immediately after crossing the vent, turn around for SPIRIT_086.

Remember the ventilation shaft in the upper floor? Now you can make your way upwards.
After leaving the vent, enter the next one on the right side. After leaving THAT vent, you can pick up your quest item but take a look into the human skull for SPIRIT_087. Next to it there is a notebook for another STORY.

Continue the quest. When passing the first door in direction to Hadley's office, turn Cahal to the room to your right. In the holding area you can collect SPIRIT_088 and SPIRIT_089.
Leave the holding area and enter the door at the opposite side. Downstairs you find SPIRIT_090.
Back to Hadley's office - before triggering the switch, you find SPIRIT_091 and another STORY.

Use the elevator and enter the first room to your right, where you can collect SPIRIT_092 and a STORY.
If you go in the other room, you find SPIRIT_093 and on the notebook another story. When following the quest you enter a cell area. In the last cell to you left side is SPIRIT_094.

In the parking lot, next to the truck, you find SPIRIT_095.

Behind Pachu'a you find you first plant (SPIRIT_096) in this level. Leaving the Caern and follow the path to your left you come across another one (SPIRIT_097).

Go back to the Caern and take the other exit. At the parting of ways choose the left side and immediately turn right at the stone pillar for SPIRIT_098.

Follow that way, cross the river and turn right. At the dead end you can collect SPIRIT_099.

Follow the quest marker till 100 meters are left. At the parting of ways take the left turn and follow the street right before you enter the tunnel. At the left side is a plant (SPIRIT_100).

Follow the quest marker till you reach the camp. Ignore the quest marker and go ahead instead.
Right before Pachu'as altar you'll see (SPIRIT_101). At the right side of the altar you find (SPIRIT_102).

Continue the quest. After talking with Declan and entering the Endron area follow the quest maker to "Outpost 2" at the right corner you find SPIRIT_103 next to a white car.
Leave that area and go to the oil pumps. Let them behind and at some stones you can crawl up to the Pachu'a altar, you'll see SPIRIT_104.

Go back to "Outpost 2", where you can open a door at the terminal. Leave that terminal room and follow the red carpet to the right. At the room behind you can collect SPIRIT_105 in form of a stone buddy.

Now make your way to "Outpost 3", where a spirit plant (SPIRIT_106) is hidden next to a tree.

Go to the right side of "Outpost 1". Near an excavator you find (SPIRIT_107).
Clean the courtyard of "Outpost 1" and enter the waiting room. In the room to your right you'll find a stone buddy (SPIRIT_108).

After cleansing all Outposts and you can go back to Declan, you come across an open gate. Left of that is SPIRIT_109. Turn to the right where that picture was taken and you'll see a hole,where you can crawl as wolf beneath a huge stone formation. Crawl to the end and you find a small cairn (SPIRIT_110).

After talking with Declan, make your way to Endrons HQ. From the courtyard you can enter a room with a curved desk. Behind that is SPIRIT_111.

At the start of the level follow the quest marker. Before you enter the elevator, you'll see SPIRIT_112.

In the room after the vent you can collect SPIRIT_113, SPIRIT_114 and SPIRIT_115. You can find these plants at the outer ring of that room.

The next plant (and SPIRIT_116) is in the room with the turret.

Immediately after you enter the next room, look to your left, where you can absorb SPIRIT_117.

After Ava tells you that Wadkins called the helicopter, you directly look at SPIRIT_118 behind a ladder.
Follow the quest marker till the next transmission and you find a plant, sprouting from cement - and so you find SPIRIT_119.

After you open the next possible door, SPIRIT_120 is directly in front of you.

Follow the quest marker and you see a conference room in front of you. Enter and cross through it for SPIRIT_121.
Continue the quest till the next dialog. In this room is a wall, which is covered with plants. In one of these plants houses SPIRIT_122.
Before you enter the elevator, you can collect SPIRIT_123 and SPIRIT_124 who are waiting for you patiently.

After the fight with the Red Talon, continue your way to Wadkins office, where you can absorb SPIRIT_125 and read another two STORIES.

When you leave the elevator, ignore the quest marker and take the path to your left to collect SPIRIT_126. Continue that way downwards and fight (or sneak) your way in direction of the quest marker. After the next transmission, in a curve, you can find SPIRIT_127.

After the talk with Ava, before you enter the elevator: turn left and go upstairs to collect SPIRIT_128.

After you reenter the building, don't follow the questmarker to your left but go straight end then turn right instead to collect SPIRIT_129 from two stone buddies.

Follow the quest marker, but before you turn right and open the door, look behind the plastic barrels, where you can cross the vents. You leave at a control room with a plant (SPIRIT_130) on the table.

When you go outside again (you'll see two turrents in front of you), go strait that line, the turrets are showing you and enter the building. When Ava contacts you, open the door to the next room. You enter a control room with two scientists and a brute. Behind the cell to your left you'll find (SPIRIT_131) in the form of mushrooms.

After you neutralized the server and used the elevator to get upwards, follow the quest marker but don't turn right but go ahead instead and use the vents to get outside. Some mushrooms (SPIRIT_132) are waiting for you.

Now follow the quest marker till you came across a reception.
Open the first steel door to your right, jump over the desks after entering the room and enter the office behind and absorb (SPIRIT_133) .
Go back, in direction of the quest marker. Don't open the steel door in front of you, but turn left into the locker room instead. There you can absorb the last spirit (SPIRIT_134) .