Once all side quests are complete, speak to Brynjolf who is wandering between The Ragged Flagon and the Cistern. Once found, follow him to the center of the Cistern where the Guild officers will initiate the Dragonborn as the new Guild Master. Once this is done Brynjolf tells you to see Tonilia as she has something for you. Once this is done the quest will complete and the Achievement / Trophy, One with the Shadows, will be awarded.
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PS3 360 If you have completed the quest Under New Management before all special jobs, Brynjolf may disappear. Rendering you unable to complete the quest and become Guild Master. Possible fix by healing Brynjolf.
If you are at the end of the thieves guild quest line and are unable to find Karliah in the Nightingale Hall, it is most likely caused by not completing enough sidequests for Vex or Delvin Mallory. If this is the case, you will instead find Karliah at the very end of the Snow Veil Sanctum, the place where she shot you. The actual bug is apparently caused by the quest Under New Management never starting, so it might be possible to fix this issue using the console command setstage TGLeadership 50. It has been tested with the NPC in Snow Veil Sanctum and Karliah has been teleported inside Nightingale Hall, moving after few hours inside the The Ragged Flagon - Cistern.
This quest may not be able to be completed if you lost all of your Thieves Guild Armor without upgrading any of it, as the dialogue option from Tonilia to receive your Guild Leader Armor will be unavailable until a piece of the Thieves Guild Armour is upgraded. A new set of armor can be found in the training hall.
The quest will prompt you to proceed to the center of the cistern. All NPCs present will accordingly gather around you, but not say nor do anything. Possible fixes:
The thief Sapphire seems to be required at the ceremony for it to begin. If you find yourself unable to complete Shadr's "Miscellaneous" quest involving Sapphire, find Shadr by the Riften Stables and quietly kill him. This will fail his quest, but free Sapphire to be present at the ceremony, allowing it to begin.(Killing Shadr, while possibly more desirable, isn't actually necessary. You can simply find Sapphire and follow her back to the Cistern)
Try to speak to Karliah and Brynjolf in front of you with you in the center of the room and the game should tell you "This person is busy". After a few seconds, the ceremony should start, with Brynjolf speaking first.
Wait for 1 hour and it should kick Brynjolf into speaking and having the quest to continue.
Talk to Tonilia and she will say you should be attending the ceremony. Go back to the center of the cistern room and the ceremony will be performed.
Be kicked out of the guild and complete the quest Reparations.
PS3 360 (As of Patch 1.4) If you have completed all of the City Influence quests and fully renovated The Ragged Flagon before you complete Darkness Returns, when you then complete Darkness Returns and return to The Ragged Flagon - Cistern, Brynjolf may walk up to you and initiate conversation, but this will not result in starting the Under New Management quest or initiate the ceremony to make you Guild Master. Attempts to talk to Brynjolf after this result in him replying that he is too busy.
Losing, selling or wearing Thieves Guild Armor appears to have no effect on this issue.
Speaking to Tonilia with or without Thieves Guild Armor on did not have any effect.
Killing Sapphire did not appear to fix this issue either.
Completing Darkness Returns before completing the final City Influence quest appears to prevent this issue from occurring and allows this quest to start correctly.
If you're in stage 4 of vampirism (without Dawnguard DLC), the NPC's (not from the Thieves Guild) that enter the room will attack you on sight. You can complete the quest, but you'll be attacked. It's much easier to just go feed and then do the ceremony. Keep in mind that you can't feed on the Thieves Guild NPC's, because they are all waiting for the ceremony. This is no longer a problem since Dawnguard.
It's possible that after you talk to Brynjolf, and he leads you to the middle of Cistern where all other high-ranking members of the Thieves Guild are present, the initiation may be skipped and be able to proceed anyway to receive your armor from Tonilia.
360 If you finish the main thieves guild questline and then proceed to talk to Brynjolf, he will incessantly say he is busy, and completing the city influence quests and using the suggested solutions above does not appear to actually change anything, making the quest unstartable. Currently, there appears to be no solution to this issue.