Who's on the Top level of clearance in the S.H.I.E.L.D. if its not Director Fury?

Question

In the pilot episode of Marvel's Agents of S.H.I.E.L.D. TV series, Agent Coulson (who isn't dead) promoted Agent Ward to clearance level 7. Lower levels, including members of The Avengers don't know that Agent Coulson is alive. Agent Coulson has level 8 clearance and is able to do powerful things like keeping a new element classified even inside S.H.I.E.L.D.

Director Fury has got Level 10 clearance who seems to be able to do anything like faking official reports and using a non-sanctioned lab to revive a dead person using classified tech. But, he doesn't look like on Top level of clearance.

• In Avengers movie, Director Fury was overridden in Nuclear Weapon launch authorization scene.

• In the episode T.A.H.I.T.I. of Marvel's Agents of S.H.I.E.L.D. TV series, the cover of the file describing how they revived Agent Coulson showed this:
  
  It says Security Level 10 or above required...

If Director Fury isn't at the Top level of clearance, who's on the Top?

Answer 1

• Agent Phil Coulson: mentions that he is level 8 early in the show, and in the final episodes of S1 of Agents of S.H.I.E.L.D.

is upgraded to Level 10 when he assumes command of S.H.I.E.L.D.

• Agent Victoria Hand: mentions that she is level 8 in the show.
• Deputy Director Hill: is listed on wikia as level 9, but is unsourced
• Director Fury is identified as the only level 10 operative in S01E14 (T.A.H.I.T.I)
• Alexander Pierce is no longer an Agent of S.H.I.E.L.D, but has a Level 10 Clearance Level.
• In Captain America: The Winter Soldier, Pierce and Fury are identified as "Alpha Level" members. Whether or not this is a reflection of their Level 10 Clearance, or something else (like the fact that Fury is the Director and Pierce is on the WSC) is left unclear.

Wikia's logic for Deputy Director Hill makes a fair bit of sense saying that Coulson and Hand are close to the top, with Fury being at a maximum level 10, but this information has not been specified yet.

As to "Who's On First Top", as @anthonygrist points out in the comments, there is really no "on top" when it comes to clearances.

Two people can have the same clearances but different authority levels. Similarly, two people can have the same authority level but different clearances. The fact Alexander Pierce has Level 10 clearance is proof that clearance level is not quite the same as operational authority within the organization.

The fact that the file folder says it requires "Level 10 Or Above" clearance is not enough to prove that any levels above 10 currently exist.

Consider the following conditional:

if x >= 10 then access_granted = true
else access_granted = false 

This does not necessarily mean that x can ever equal 11 or even 10.1. It just means that my code is not specifically looking for an exact value of 10 and only 10.

If for some reason an additional level of clearance was ever added to S.H.I.E.L.D's system, anyone 10 or above would be allowed access without having to go restamp all the files.

It's also entirely possible that something like a standard adjustable stamp was used. They typically have a standard bit of text or two and selectable values as evidenced by this recent publicity photo which appears to have identical stamps aside from the clearance level number.

Answer 2

Even Nick Fury Has A Boss

Although sometimes he kinda ignores them. In the cinematic universe, the entity that most directly sits "above" Fury is the World Security Council:

While the WSC, and other high-level political powers, are not actually part of the SHIELD hierarchy - they do have command and control authority over SHIELD. So while Nick Fury may have Clearance Level 10 - it is well within the power of the WSC to simply withhold information from Fury if they see fit.

In other words - the WSC can make the clearance level moot. Or to put it another way - within SHIELD it is nearly impossible to keep a secret from Fury. Outside of SHIELD, it becomes a little easier.

The structure is meant to provide a watchdog over SHIELD, however it also helps lead to the events of Captain America: Winter Soldier.

Answer 3

The override was performed by the WSC in a watchdog position (to watch over SHIELD). Even if they cannot directly override Fury it is possible they were committed to a radio-silence mission by someone on the same level as Fury. Either way, this can happen somehow.

The document seems to be made according to a template, and for level 10 the statement is meaningless unless an eleventh level will ever be made. In which case it will be useless for level 11.

Don't forget that there may always be more levels and complexities hidden from anyone ever shown on screen, if the writers need there to be. The level 10 or above is a goof. The WSC and how they could launch a nuclear fighter whilst evading Fury is mysterious but it was plot essential. If ever plot makes need, additional levels are waiting in the unknown. (Note: nobody can give you an in-series conclusive answer, because it could be secret from all those we know.)

Answer 4

Officialy Fury is the highest ranking S.H.I.E.L.D operative at level 10. The World Security Council can override Fury's ruling on Alexader Pierce's call. Some areas or files as seen in Captain America 2, require Alpha level access which has been shown to be posessed only by Fury and Pierce and requires 2 alpha level operatives to use alpha level systems or data

Answer 5

Navy ships have an Executive Officer and a Captain. Both have the highest rank on the ship-but their duties are different. Captains run the ship-execs counter the captain when needed. It seems the similar logic is found here.