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Brynjolf is convinced Mercer Frey intends to perform one final heist before departing Skyrim for good. According to the plans I discovered in Riftweald Manor, he's after the "Eyes of the Falmer", two gems of enormous value. If we have any hopes of intercepting Mercer, we need to proceed to their location immediately.— Dragonborn
Karliah and the Dragonborn speak to Brynjolf at the Cistern and convince him that Mercer indeed betrayed them all. Brynjolf cannot believe this, but opening the Guild Vault together with Delvin Mallory (two of the three with the keys to open the vault), they discover the vault completely plundered. So there cannot be any doubt of Mercer's guilt any longer.
Speak to Brynjolf
Brynjolf wants to know everything the Dragonborn has learned about Karliah: the subjects of her involvement with the Goldenglow Estate and the Meadery in Whiterun come up, that she, Mercer and Gallus were part of the Nightingales, and that indeed Mercer killed Gallus and not Karliah.
The Guild is now out for revenge, but Mercer is nowhere to be found. Brynjolf is convinced he is still planning one final heist and information about it should be present at Riftweald Manor, Mercer's retreat in Riften. Apparently the manor is guarded by Vald, someone Vex knows.
Speak to Vex about Vald (Optional)
Talk to Maven about Vald's debt
The Dragonborn can choose to follow this path, avoiding bloodshed, see the side-quest Vald's Debt, as detailed below.
Maven tells the story of a job regarding the retrieval of the very valuable Quill of Gemination that Vald botched up, losing the quill in the process. To repay the debt Vald ended up having to work for Mercer.
Locate the Quill of Gemination under Lake Honrich
As it turns out the quill was transported by boat from the western end of Lake Honrich, but the boar hit some rocks and sank somewhere between the Goldenglow Estate and the Riften docks. It is up to the Dragonborn to dive for the item.
Tip: Exiting the docks, follow the line between to ship at the docks right to the ship docked at the Goldenglow Estate in the west, and dive to discover the wreck of the small boat that sank here.
At the wreck of the boat open Vald's Strongbox to retrieve 120 and the Quill of Gemination.
Bring the Quill of Gemination to Maven
Return the quill to Maven who will not be too overjoyed since she had already given up on it, but none-the-less keeps her promise and purges Vald's debt to her in writing: Vald's Debt.
Go to the back side of the Riftweald Manor where Vald is guarding the house. Avoid entering the yard on your own accord since Vald will immediately attack. Wait until Vald walks near the back gate and talk to him instead. He will not be able to believe what the Dragonborn was able to do for him by handing over Vald's Debt document. He gives the Dragonborn Mercer's House Key as a small sign of gratitude.
Shoot the mechanism to lower the ramp (Optional)
Now as it turns out all doors to the manor are blocked from the inside, only on the back of the major, above the yard Vald was guarding, can the mechanism for a ramp be shot to lower it. Only the door at the top of the ramp can be unlocked with the key or lockpicked.
Note: Shooting the mechanism is not actually optional at all, it is the only way in, other than some judicious use of jumping and Whirlwind Sprint to get to the balcony up there.
Infiltrate Mercer's house
Entering Riftweald Manor the Dragonborn stumbles into two bandits, probably here to loot the place. On a table on the lower floor the To The Owner note reveals that Mercer had some work done on the manor mentioning not only a ramp mechanism outside, but also a hidden door. Nearby a Suspicious Cabinet opens via False Back Panel to a second cellar that leads into the sewers.
Discover evidence of Mercer's location
Following the path laden with many traps the Dragonborn finally makes it to a small room with the searched for evidence: Mercer's Plans. And a mysterious note, Many Thanks, hints at some form of reward, placed at the usual location, Mercer received for retrieving some special item.
Note: On the same table there are gems worth around 3100 , a sword called Chillrend and the Bust of the Gray Fox. The latter unusual trinket is something Delvin Mallory will very much be interested in purchasing.
Speak to Brynjolf
The secret passage exits into the Ratway Vaults. Return with the plans to Brynjolf at the Cistern. As Brynjolf explains Mercer is indeed after the Eyes of the Falmer, and the Dragonborn should talk with Brynjolf and Karliah about the next step in Trinity Restored.