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In the April 2020 issue of The Atlantic, George Packer offers this interesting but brief discussion of the term deep state in his article "The President Is Winning His War on American Institutions":

To Trump and his supporters, the swamp was full of scheming conspirators in drab D.C. office wear, coup plotters hidden in plain sight at desks, in lunchrooms, and on jogging paths around the federal capital: the deep state. A former Republican congressional aide named Mike Lofgren had introduced the phrase into the political bloodstream with an essay in 2014 and a book two years later. Lofgren meant the nexus of corporations, banks, and defense contractors that had gained so much financial and political control—sources of Washington’s corruption. But conservatives at Breitbart News, Fox News, and elsewhere began applying the term to career officials in law-enforcement and intelligence agencies, whom they accused of being Democratic partisans in cahoots with the liberal media first to prevent and then to undo Trump’s election. Like fake news and corruption, Trump reverse-engineered deep state into a weapon against his enemies, real or perceived.

A quick Google Books search indicates that Mike Lofgren writing in 2014 was by no means the first author to deploy the term deep state in a political sense. Here is how the term appears in Peter Dale Scott, The Road to 9/11: Wealth, Empire, and the Future of America (University of California Press, 2007):

But this book also focuses on something else: the top 1 percent's direct or indirect control of certain specific domains of government, beginning in the 1940s with the creation of CIA. It is a story that looks beyond the well-defined public entities of open politics to include the more amorphous and fluid realm of private control behind them. This realm of wealthy private influence, the overworld, is a milieu of those who either by wealth or background have power great enough to have an observable influence on their society and its politics. Those parts of the government responding to their influence I call the "deep state" (if covert) or "security state" (if military). Both represent top-down or closed power, as opposed to the open power of the public state or res publica that represents the people as a whole.

I argue in this book that the power of the American public state needs to be revived and its out-of-control deep state radically curtailed. I am not an opponent of deep states per se: publics are not infallible and sometimes need to be opposed. But in our current crisis the proper balance between the public state and the deep state has been lost, and the deep state's secret top-down powers have become a major threat to democracy. A well-functioning deep state serves to impose needed wisdom and discipline, but in recent years America's unchecked deep state has been imposing both folly and indiscipline.

Still, the phrase doesn't seem to have been widely used in U.S. political discussions during the first decade of the 2000s. William Safire, Safire's Political Dictionary (2008) has entries for deep background, deep freeze, and deep-six, but not for deep state. The Oxford Dictionary of American Political Slang (2004) is likewise silent about the term. Even as recent a collection of U.S. political terms as Chuck McCutcheon & David Mark, Dog Whistles, Walk-Backs and Washington Handshakes: Decoding the Jargon, Slang, and Bluster of American Political Speech (2014) doesn't address deep state at all.

Presented with this seeming vacuum of information, I am looking for answers to the following questions about deep state as a U.S. political term:

  1. What was the original meaning of deep state as applied to politics, and when did the term arise in that context?

  2. When did the sense of the expression shift (if indeed it did shift) from that original meaning to the meaning (according to George Packer) "the nexus of corporations, banks, and defense contractors that had gained so much financial and political control [in the United States]"?

  3. When did the expression shift again to begin referring to supposed institutional (that is, government-embedded) opponents of right-wing politicians and their policies?

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Background in gizli devlet and derin devlet

Turkish gizli devlet, translated into English 'secret state', foreshadows and overlaps with Turkish derin devlet, 'deep state'. The former shows up as early as 20 Oct 1955 in the title of a pamphlet:

The delegation asked the authorities to confiscate four anti-Jewish publications which recently appeared on the stands here. One of them is the "Secret State and Program of Conspiracy" by Cevat Rifat Atilhan, a notorious anti-Semte [sic].

That translation of gizli devlet shows up again in the title of a 1957 pamphlet by the same author in 1970 (The National Union Catalog 1956 through 1967):

Gizli Devlet ve porgrami The secret state Istanbul?

The (check-out with free account) 1999 Warrant for genocide: key elements of Turko-Armenian conflict (Dadrian, Vahakn N), cites a 1996 book by Suat Parlar, The Secret State: From Ottoman days to the present.

In this context of gizli devlet, the Turkish 'secret state', alongside frequent association of the English phrase 'secret state' with state-level security and intelligence forces, Robert D. Kaplan, a contributing editor for The Atlantic Monthly (later The Atlantic), details a political sense of derin devlet, Turkish for 'deep state', in "A different democracy" (paywalled; 01 Jul 1998, The Boston Globe):

...what Turks call "the deep state", symbolized by the military, hides behind the white-lie facade of the superficial civilian cabinet.

Kaplan goes on to observe, of the Turkish military, that it

is less a fighting machine than the country's best-organized, most respected secular institution, with deep historical roots.

Kaplan reports that at the time, the term derin devlet, 'deep state', was used to describe the military's covert response to these Turkish political events:

In 1996, a democratically elected, hopelessly divided Parliament...led to a weak minority government of Muslim fundamentalists. ... The Turkish military...began undermining [the] government through intimidation, press briefings, and regulations that curtailed the business activities of [the government's] religious supporters.

Kaplan's is the earliest significant use of 'deep state', the translation of derin devlet, that I found. It is followed by a fair sprinkling of other uses:

  • a (paywalled) 2000 USA newspaper article by Stephen Kinzer, "Pope's attacker carries secrets home",

    "He must know a great deal about the connection of the extreme right wing to intelligence services, police and other elements of what we call 'deep state'."

  • a (check-out) 2001 USA book by Daniel G. Bates, Peoples and cultures of the Middle East,

    In Turkey, for example, peope complain bitterly about the so-called "deep state" or the perceived collusion among business, military, and political leaders.

  • a (paywalled) 2001 British newspaper article by Chris Morris, "Turkey jails spy and ex-police chief for running hit squad",

    ...it sparked genuine fears among ordinary Turks that gangs within the state had been given unfettered control, and could be a threat to democracy. Suspicion of what Turks call "deep state links" is still extremely strong.

  • another (paywalled) 2001 British newspaper article by Chris Morris, "Gang rule keeps Kurdish lands lawless",

    [Diyarkabir's] popular police chief, Gaffir Okkan...was assassinated in a professional ambush in the city centre.
    ....
    The official explanation is that Okkan was murdered by the radical Islamic group Turkish Hizbullah. On the streets of Diyarbakir, however, nearly everyone seems convinced that what they call the "deep state" was involved.

  • a (paywalled) 2002 Canadian article by Patrick Graham, "Troubled Turkey goes to polls",

    This is part of a turf war between the Islamists and Turkey's long-established secularists, led by the army, who remain loyal to the legacy of the country's founder, Kemal Ataturk. The last time an Islamist government got out of line it was removed by the military in what analysts call a post-modern coup....
    The military, along with judges and the bureaucracy, are the ultimate arbiters of Turkish life and would prevent Islamic fundamentalism from taking over Turkey no matter what the cost.
    But the legitimacy and reputation of the "deep state," as some call it, suffered badly in the 1990s....

  • a 2003 essay by Soli Özel, "Turkey at the polls: After the tsunami",

    At the scandal's heart was the lawless "dirty war" that Turkey's shadowy "deep state" had been waging in the southeast.

  • a (paywalled) 2003 British newspaper article by Helen Smith, "New breed of Islamic politicians start to find their feet",

    Mr Erbakan's humiliating removal and the prohibition of his Welfare party in 1998 apparently convinced the AKP that provoking Turkey's "deep state" — the military, bureaucracy, media and judicial circles that make up its ruling elite — would be political suicide.

  • a (paywalled) 2003 British newspaper article by Jonny Dymond, "West must help Turkey fight back",

    The rubble had not been cleared from the two synagogues bombed last weekend when the Briutish consulate was ripped apart and the HSBC headquarters destroyed.
    ....
    Some theorise that the military-bureaucratic complex — the "deep state", the government within a government — had allowed the attacks to happen.

Two uses of 'deep state' in 2004 represent the term in its original Turkish sense. One is a footnote in a USA Naval Postgraduate School thesis by Michael Naoum, "The Greek-Turkish rapprochement process, 1999-2004: paradigm shift or EPI-phenomenon",

The forces described by Onis are also known as the "deep state."

The other 2004 use is in a (paywalled) newspaper article, "Struggle for the soul of Islam":

In Turkey the government and the state are not always synonymous. The state bureaucracy can prove hard to control for even the most adept party in power. And Turkey's so-called deep state, made up of ruling elites from the military, judicial branch, business and media, has long wielded tremendous power behind the scenes.

A 2005 use in a book by Speros Vyronis, The mechanism of catastrophe: the Turkish pogrom of September 6-7, 1955, and the destruction of the Greek community of Istanbul, suggests that Turkish derin devlet is simply a more recent term for what was called gizli devlet:

Governmental control of Turkey's judicial system involved the bondage and corruption of the latter, as well as the tradition of the "gizli devlet," that is, the "hidden state" (or, as it's been called more recently, the "derin devlet," or "deep state").

Five more uses in 2005 confirm that the sense of the Turkish derin devlet, 'deep state', encompasses not just intelligence agencies, but intelligence agencies acting in cahoots with assorted others, including gangsters, drug dealers, and other government agencies and branches, outside the rule of law.

In 2006, a book by Peter Galbraith, The end of Iraq: how American incompetence created a war without end mentions the Turkish 'deep state':

Some Turkish strategic thinkers, including those within the so-called "deep state" comprising the military and intelligence establishments, see Iraqi Kurdistan as a potential asset.

Extension beyond Turkey

Ryan Gingeras, in a 04 Feb 2019 article, "How the deep state came to America: A history" (Texas National Security Review) offers an in-depth account of "the history of how and why the phrase entered American parlance." He observes that the "first scholarly effort to internationalize the concept of the deep state came in an essay pubished in 2009 by Norwegian scholar Ola Tunander", but goes on to recount that

Tunander presented this view of the deep state before a conference held in Melbourne in 2006. ... Attending the conference was the scholar perhaps best known for popularizing the concept of "parapolitic," Peter Dale Scott. Up until that point, Scott later explained, he had never heard of the deep state but was taken by Tunander's analysis of Italy and its applicability elsewhere. "I was very gratified," he told me in 2007, to realize "how closely, how very closely, my analysis of America fit Ola Tunander's [thinking] of both America and other states."

The history by Gingeras accurately details when the sense of 'deep state' shifted from its original sense, a straightforward reference to the Turkish concept, to a broader application to other state political systems.

The extension of the term 'deep state' to USA political systems, for example, began to appear in Peter Dale Scott's works, from Tunander's generalized concept, starting in 2007. For example, the term appears several times in a 2007 essay (dated 2004 at archive.org, but internal references date to 2007, so the essay must have been published that year or later), "9/11, JFK, and War: Recurring patterns in America's deep events" (bolding mine; see also quotes in the OP from Scott's 2007 book, The Road to 9/11):

  If history is what is recorded, then deep history is the sum of events which tend to be officially obscured or even suppressed in traditional books and media. Important deep events include the politicial assassinations of the 1960s, Watergate, Iran-Contra, and now 9/11. All these deep events have involved what I call the deep state, that part of the state which is not publicly accountable, and pursues its goals by means which will not be approved by a pubic examination. The CIA (with its on-going relationships to drug-traffickers) is an obvious aspect of the deep state, but not the ony one, perhaps not even the dirtiest.
  When I talk of a deep state, this term (as opposed to others, like deep politics), is not my own invention. It is a translation of the Turkish gizli devlet, or derin devlet, a term used to describe the networks revealed by the so-called Susurluk incident of 1996, when the victims traveling together in what became a deadly car crash were identified as "an MP, a police chief, a beauty queen and her lover, a top Turkish gangster and hitman called Abdullah Catli."

Later uses in the same essay establish that Scott, when referring to the 'deep state', sometimes merely means 'intelligence agencies'. For example, on p 4:

3) Commission recommendations to increase power of intelligence agencies, or deep state

Scott, however, again makes the connection between the gizli devlet and the deep state in Turkey on p 21:

The pattern moreover is that exhibited by the gizli devlet or deep state in Turkey, where a Parliamentary Investigation into the Susuruk Report concluded that the deep state had used the drug-trafficking Grey Wolves and fomented conflicts in the 1970s between the Turkish right and left. The alliance between the deep state and drug traffickers has surfaced in other countries as well, incuding France, Italy, Mexico, Panama, Pakistan, Taiwan, and Japan.

Scott, according to his statement in a 2007 podcast interview with Gingeras, credits Tunander with the original broader application of the term 'deep state' beyond Turkish political systems, to USA and other nation's political systems.

Appropriation degenerates the concept

The 2019 Gingeras article in Texas National Security Review points to the amplification beginning in 2008 of the 'deep state' from Scott's 2007 book, The Road to 9/11, as the initial route to popularization of the term:

It was as a result of this book, and the exposure [Scott] received thereafter from Alex Jones and others, that many Americans first entertained the notion that a deep state lorded over the United States.

(The Southern Poverty Law Center describes Alex Jones as "almost certainly the most prolific conspiracy theorist in contemporary America.")

Gingeras notes the fuzziness of the 'deep state' concept:

Yet defining what exactly constitutes a deep state, let alone documenting its existence, is another matter. The story of how the deep state entered American consciousness underscores the inexact science and fancifulness that hampers any discussion of secret states and shadow governments.
....
Since it was first coined over 20 years ago, no precise definition for what it means has fully taken hold. Use of the phrase generally denotes belief in an informal or parallel government that exists to countermand legitimate, usually more democratic, institutions. Who constitutes this shadow government depends widely on whom you ask and where or when the discussion takes place. While the term originated with reference to the hold security institutions have over state and society (such as in Turkey), the list of deep state actors can include social groups accused of exploiting everyday citizens, like the mafia, “big business” or ideological extremists.

Michael Lofgren's use of 'deep state' in his 2014 essay, "Anatomy of the Deep State" represents a re-appropriation of the concept first developed by Tunander, then particularized by Scott, and finally degenerated by Alex Jones and company. Lofgren's belated 2014 appearance in the 'deep state' circus ring, along with the earlier hand-off of US application of the term from a left-aligned scholar to a right-aligned conspiracy theorist, supports and reinforces Gingeras's 2019 conclusions, among them that

More often than not, the search for a deep state provides license for those seeking to conflate and marginalize political dissidents and opponents.

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Searching Ngram hits, the earliest use of the term in the sense of a political "inner circle" is in 1997 with regard to Turkey, as JEL suggests:

The latter is fragmented and has waned considerably DOGU ERGlL Clandestine The 'deep state' remains hidden from the public. It is staffed by the security personnel. Its activities and the driving principles behind those activities are not ... Turkish Daily News

And subsequently I don't see it mentioned again until a book first published in 2003, Turkey: The Quest for Identity.

Searching much further for uses of the term is difficult, because it is used in physics, psychology, Buddhist meditation, and sleep research, among other areas. Uses in the political sense are rare, relatively speaking.

But it appears that this political sense was used almost exclusively to refer to the Turkish situation until around 2014, when it began to be applied more broadly to the security regimes of other nations, and when some conspiracy theorists adopted the term to be used to refer to a supposed inner circle of the US government.

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