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During the ending of Mission: Impossible - Rogue Nation, after reinstating IMF William Brandt (Jeremy Renner's character) says to Hunley "Welcome to the IMF...Mr. Secretary." and both smile and credits roll.

What does it signify? Was Hunley made the new secretary of the IMF or was he the secretary beforehand and was in on it from the start and helping them (Ethan and his team) to pull out a bluff to go undercover?

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Was he the Secretary beforehand and was in on it from the start and helping them (Ethan and team) to pull out a bluff to go undercover?

No.

Wikipedia makes this clear. The whole IMF (which seems to be a fairly large organisation) was disbanded and incorporated into the CIA.

CIA Director Alan Hunley and IMF Field Operations Director William Brandt testify before a Senate committee. The IMF, currently without a secretary in charge, is controversial because of its destructive methods and various misconducts. Hunley succeeds in having the IMF disbanded and absorbed into the CIA.

Afterwards...

Hunley, having witnessed an IMF operation's success firsthand, returns with Brandt to the Senate committee meeting and convinces them to restore the IMF by covering for Hunt and his team. After the meeting, Brandt congratulates Hunley, who is now the new IMF Secretary.

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