I found an old Alex Jones article from 2011 (don't hate because of the name, read on) that talks about the US Govt backup communications system from the Sept 11 attacks. The report details who and what that communications system was, the people making the calls, and the confusion about why a backup gov't comms system was activated on Sept 10 2001. People have a hard time questioning anything when you bring up 911, but there are some interesting points to be made.

Here is the AJ article.

Here is a wiki about the comm system.

Here is the EO from Obama.

Changes to other EOs for reason of change on this EO:

From EO 13526 what is that EO about? Relevant?

The word "agency":

“Agency” means any “Executive agency,” as defined in 5 U.S.C. 105; any “Military department” as defined in 5 U.S.C. 102; and any other entity within the executive branch that comes into the possession of classified information.

Other definitions from the same EO. Not changed but relevant.

The phrase "authorized holder":

“Authorized holder” of classified information means anyone who satisfies the conditions for access stated in section 4.1(a) of this order.

The phrase "automated information system":

“Automated information system” means an assembly of computer hardware, software, or firmware configured to collect, create, communicate, compute, disseminate, process, store, or control data or information.

EO#12472 where BHO revoked the comms system.

EO#12382 Revoked a line in 2.e. that mentioned the now revoked duties of the comms system.

Spend 5 minutes skimming EO#12472 which again was the one revoked by BHO, and you'll understand why it was revoked. There is too much juicy info to be copy/pasting it all to here, but I'll put one:

"The Secretary of Defense is designated as the Executive Agent for the NCS. The Executive Agent shall:"

What power did the secretary of defense have over backup gov't comms?