Act 3 is very short, and just encompasses the final story section of the game. At this point you can clean up all remaining other side activities, or finish the story and complete everything after. Once you finish the story you are placed back in the final story location.
Act 3
Investigation #6 – Into the Unknown
Head through the doorway and defeat the enemies until they stop appearing in the room. You can then pull the lever to the right to continue.
Walk through the tunnel and when you reach the save point you’ll earn 
Long and (not so) Winding Road. Continue forward and in the next room you can pick up an Amine Prism – Rho and Scroll – Failsafe off the central pillar, then Orbs – Cobalt, Gold, Emerald, Crimson from the other four pillars.
Continue forward along the path and when you enter the next area you’ll earn Well-Traveled for entering all locations.
In this room you need to make your way around the area, defeating the giant Hollow enemies and placing the four orbs that you picked up. First, follow the path around to the north where a yellow Hollow is roaming. Defeat it, then interact with the statue that has the Rage symbol and place the Orb – Crimson.
Continue clockwise following the wall on the left to reach the green Hollow enemy. Defeat it, then in the statue that has the Grief symbol place the Orb – Cobalt.
Continue moving around the area clockwise. You can go toward the Timeloop, then open a gate leading into the center of the area. On the north side of the platform you can find a ladder leading to the top, which will allow you to reach the red Hollow enemy. Defeat it, then climb the scaffolding up and to the right, then around the left side at the bottom to reach the statue that has the Terror symbol and place the Orb – Emerald.
Finally go back up the scaffolding, then go toward the final blue Hollow enemy. Defeat it, then at the statue with the Ecstasy symbol place the Orb – Gold.
Make your way up to the Timeloop and enter it. Interact with the drone and use Amine Prism – Rho to close it.
After the Timeloop disappears, go to the desk to the south where you can pick up Baseball Cap – Gilded.
Interact with the pedestal and place the Heirloom Necklace to complete the story, earning Redemption.
Cleanup
Reload your save and you will be back at the last save point you interacted with, and can travel back to the APC from it.
In the APC turn in your two newest Research Items to receive Sworn to Secrecy.
We’ll now work through the remaining areas in order, cleaning up the last things that need to be done.
Senedra Forest
Vault of the Copse – From the APC go west up the hill to the OMSIF camp you went to at the start of the game. Behind the tent is a cave you can walk into where you can find the vault door. Open it by changing the dials to: Terror symbol, figure 8, Rage symbol, Circle with Spikes.
Inside the vault you can pick up a bunch of items. On the left: Tome – A Bitter Triumph, Amine Prism – Sigma, and Glyph #61: Gluttony. On the right: Letter – To Rosetta, Glyph #62: Overwhelm, Glyph #63: Feed on Fear, Parchment – Preparations, and Glyph #64: Wave of Wrath.
Mystery #9: Lymbic Door – Senedra, Hilltop – Go back to the APC and follow the right wall around the hill to the ruins at the top where you can find a blue Lymbic door. Insert Lymbic Rods – Grief, V and Grief, Z to open the door and complete the mystery.
Timeloop: Senedra – Hilltop – Enter the room to find the Senedra Forest Timeloop, with the last accessible Timeloop Guardian beside it. If you hadn’t already, use the Guardian Detector to find the others, then come back and enter the Timeloop, interacting with the drone and using Amine Prism – Sigma to close it. Rewards Glyph #65: Waves of Grief – Enhanced, Glyph #66: Waves of Wrath – Enhanced, and Relic #25: The Omen of Oblivion.
Research Item: Ancient Scroll – In the room with the Timeloop you can pick up three items: Drone Module: Rearguard, General Firion’s Journal, and this research item.
Return to the APC and turn in this Research Item to earn Historian.
Acasa Marshes
Mystery #3: The Captain’s Office – In Jova go back to the drunk soldier in the center of town and trade him the Bottle of Mead – Full to receive Key – Jova Office.
Go up to the roof of the building near the entrance of town and you can walk through to the other side, then use the Key – Jova Office to open the door, completing the mystery.
Enter the room and you can pick up three items: Research Item: Prison Manifest, Recording – Vaas’ Plan, and Baseball Cap – Sabinian.
If you haven’t already, go through your inventory and equip each of the hats. After equipping them all at least once you’ll earn 
Passion for Fashion.
Vault of the Mire – Go northeast of town back to the OMSIF camp, then around the back to the cave where you passed the Vault door earlier. Change the dials to the following: Rage symbol, Ecstasy symbol, Terror symbol, Grief symbol.
Inside the vault you can pick up the following items, on the left: a Greatsword of Rage, Twin Axes of Ecstasy, Tome – Anson Lingen, The Wandering Mason, Tome – The Endless Horror, and 5 x Tuning Stone – Strong. On the right: Parchment – Penance, a Polearm of Terror, Parchment – A Grand Stratagem, a Sword of Grief, and Relic #26: Heart of the Griffon.
Mystery #42: Safekeeping – Go to the east side of the area where the entrance to Panthem Abbey is. Opposite the entrance is a doorway where you can find a chest. Use Key – Rustic to open it and receive Relic #27: The Panoptic Eudemon, completing the mystery.
Return to the APC and turn in your Research Items to obtain any bronze trophies you may still have been missing, along with 
Well-Read for researching all items.
Vyssa Hills
Mystery #33: Pilgrimage – Make your way northwest back through the stone tunnels until you reach the top of the area with the Hollow statues where the Timeloop was located. In the ruins you can find a chest and use Key – Barrel to open it and receive 2 x Tuning Stone – Steady and Glyph #67: Lymbic Slivers – Enhanced, completing the mystery. You should also earn Super Sleuth for completing all mysteries.
Talju
Timeloop: Talju – Go to the northwest corner of town past the barn where you can find the Timeloop. Enter and interact with the drone, using an Amine Prism – Theta to close the Timeloop. Rewards Glyph #68: Nightfade – Elite, Glyph #69: Chromatic Shield – Elite, and Relic #28: Entropic Enigma.
At this point you will have cleared all Timeloops, but to earn Legend of the Phol you also need to now go through each area and kill every Hollow, after which they won’t respawn, so you are completely clearing the game of enemies. Unfortunately the Guardian Detector won’t point you towards remaining enemies, but you can see areas where you have defeated all enemies if they show a Threats: Clear text on their info in the APC map menu.
Marastan
Vault of the Beck – Go to the southeast of the area past the ruins and into the cave with the tunnel leading to their center. In the tunnel you can find the vault door, switch the dials to: Circle with spikes, Eye, Figure 8, U.
Inside the vault you can pick up the following items, on the left: Tome – The Ascendance of Hellion Lodges and the Birth of Lymbic Aesthetics, Part 3, Parchment – Regret, Glyph #70: Rage Spike – Elite, Amine Prism – Rho, Relic #29: Orison of Valour. On the right: Glyph #71: Frightful Ambush – Elite, Painting – Queen Raveta, Glyph #72: Waves of Grief – Elite, Glyph #73: Masochistic Delight – Elite.
After picking up that relic you have all 29 and should earn Antiquarian, along with 
Hero of Hadea.
