Standalone Complex is based on the idea that:

The Stand Alone Complex is a philosophical construct; A copy of something that does not exist, or to make it clear, a copy that does exist but the thing it copies (The Original) does not exist.

and also we have it in the Matrix.

But if we look closer at the 3rd stages of sign-order in "Simulacra and Simulation", we get the same idea and same plot setting.

The third stage masks the absence of a profound reality, where the simulacrum pretends to be a faithful copy, but it is a copy with no original. Signs and images claim to represent something real, but no representation is taking place and arbitrary images are merely suggested as things which they have no relationship to. Baudrillard calls this the "order of sorcery", a regime of semantic algebra where all human meaning is conjured artificially to appear as a reference to the (increasingly) hermetic truth.

Could we say the both series use this Idea?

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    You can say The Matrix is based on the comic strip Garfield. – Wad Cheber stands with Monica Jun 18 '15 at 1:13
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    "and also we have it in the Matrix" How so? Earth did look like that in the era the Matrix is copying. – Hypnosifl Jun 18 '15 at 1:55

I can't speak to Ghost in the Shell, but it's extremely likely that The Matrix, at least, was influenced by "Simulacra and Simulation"; the film is very closely associated with that book:

  • A copy of the book makes a brief appearance in the first movie in the series, as the hollowed-out container where Neo keeps his hacked programs:

    Some light reading

  • A 1996 draft of the script explicitly calls out Baudrillard moments before quoting from his book:

    Morpheus: This is the Chicago you know. Chicago as it was at the end of the twentieth century. This Chicago exists only as part of a neural-interactive simulation that we call the Matrix.

    We GLIDE AT the television as he changes the channel.

    Morhpeus: You have been living inside Baulliaurd's [sic] vision, inside the map, not the territory. This is Chicago as it exists today.

    The sky is an endless sea of black and green bile. The earth, scorched and split like burnt flesh, spreads out beneath us as we ENTER the television.

    Morpheus: 'The desert of the real.'

    And from the 1998 shooting script (PDF link) we have two shout-outs:

    1. The image from my first bullet point:

      [Neo] closes the door. On the floor near his bed is a book Baudrillard's Simulacra and Simulations. The book has been hollowed out and inside are several computer disks.

    2. Another version of the scene quoted above:

      Morpheus: This is the world you know. The world as it was at the end of the Twentieth Century. It exists now only as part of a neural-interactive simulation that we call the Matrix.

      He changes the channel and we see a very different city as we enter the television.

      Morpheus: You have been living inside a dreamworld, Neo. As in Baudrillard's vision, your whole life has been spent inside the map, not the territory. This is the world as it exists today.

      In the distance, we see the ruins of a future city protruding from the wasteland like the blackened ribs of a long-dead corpse.

      Morpheus: 'The desert of the real.'

  • Many sources claim that it was required reading on-set;

    1. A 2003 article in The New York Times:

      This is why Mr. Baudrillard's book "Simulacra and Simulation" is so closely associated with [The Matrix] (some cast members were asked to read the book, which Morpheus, the rebel leader, also quotes).

    2. 2007 article from Inside Higher Ed (emphasis mine):

      A segment on National Public Radio included a short clip from [The Matrix] soundtrack in which Lawrence Fishburn’s character Morpheus intones the Baudrillard catchphrase, “Welcome to the desert of the real.” The cover of Simulacra and Simulation -- in some ways his quintessential theoretical text, first published in a complete English translation by the University of Michigan in 1994 -- is shown in the first film. Furthermore, the Wachowski brothers, who wrote and directed the trilogy, made the book required reading for all the actors, including Keanu Reeves.

    3. An undated interview (clip on YouTube from 2010) with Keanu Reeves:


      Reeves: [...] said "Okay, we'd like you to play Thomas Anderson; Neo." I had to read Baudrillard; I had to read "Out of Control", which is about systems evolution, robots; and then there was another book which was... "Evolutionary Psychology". Those were three books that they wanted me to read before I even opened up the script.

    4. A 2000 interview with Rolling Stone:

      The film's directors, Larry and Andy Wachowski, said they were looking for a maniac who would do what they needed: "And," Larry said, "Keanu was our maniac." They gave him some books to read: The Moral Animal, about evolutionary psychology; Simulacra and Simulation, by Jean Baudrillard ("Oh, it's fun! It's fun!" says Reeves); and Kevin Kelly's Out of Control, a book about machines and social systems. "They just said, 'Go read, go read, go see what it does,'" says Reeves. "I think they gave me the phenomenal world, the internal words and the simulations that occurred in that."

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Ghost in the Shell is based not only on Simulacra and Simulation but a number of other Philosophical works and ideas especially, Jacques Derrida's concept of iterability. "For Derrida, iterability does not simply signify repetition as in ‘reiteration’; rather, every iteration is an alteration, or a modification of the same. At the same time, iteration depends on a minimal remainder and illusion of an identity of the same so that repetition can be recognized in the first place. Iteration introduces new contexts and variety into the constitution of the same." With that being said, note the ambiguous figure of the Laughing Man that appears throughout the series illustrates the aporia present in all performative acts. The laughing man, a singular figure can be appropriated by the process of iterability and achieve a memetic status beyond the ownership of the original--assuming, of course, that it is accurate to speak of an original at all.

See: http://www.blackwellreference.com/public/tocnode?id=g9781444333275_chunk_g978144433327510_ss1-95

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