The canon of a role-playing game is that which affects continuity. It's whatever gets treated as real and significant, within a series of published works or within your campaign.
In the process of writing Delta Green, the trio of Detwiller, Tynes and Glancy were aware of how Vampire: The Masquerade and the rest of White Wolf's World of Darkness had painted itself into a corner. The "Old" or "Classic" World of Darkness is famous for embracing the concept of metaplot, with outcomes and interconnections to the individual plots suggested by its sourcebooks. White Wolf's approach has drawn a lot of criticism for being too rigid in this regard, essentially railroading the entire player base to sell more books. However, even the end of the world in 2004's Time of Judgement books offers three to five scenarios for each of eight WoD games, each one with different outcomes, and with wildly varying degrees of connection to the preceding sprawl of material.
The authors and fans of Delta Green have arguably overreacted to the centralized approach of White Wolf, which was the major competitor when the first sourcebooks were written. Both Tynes and Glancy have stated the focus of Delta Green is on the group of players: “Every published role-playing game is a work of collaborative fiction between the authors, the players and the referee. The story doesn’t really exist until the players and referee execute it around their game table.”1 In this perspective, the canon is everything that gets presented as a fact in an individual campaign.2 The ultimate responsibility for building a coherent universe is thereby shifted from the authors to the players.3 This puts a heavy workload on the GM.
If Majestic-12 is just too X-Files, or the Karotechia is overly “pulp,” or Stephen Alziz [sic] is way too deus ex machina, then I see no reason why a Keeper has to use them. A Keeper could just as easily drop Delta Green itself and run a campaign based on SaucerWatch, Phenomen-X or PISCES.4
Ironically, there are contradictions to the stated, decentralized approach. Delta Green was created with a tremendous ambition to achieve coherence and believability, something Tynes had been missing from the experience of basic Call of Cthulhu.5 Elements like the Karotechia and Delta Green have deep historical connections. This makes them more credible, and serves the additional purpose of making them easy to use together. For all intents and purposes, the sourcebook material forms a canon, against which the authors themselves clearly distinguish other material.6 According to Glancy, this literary canon only affects the initial setup,7 and even then, its influence is necessarily a matter of choice for the GM. By necessity, this is equally true in literally every other RPG. Authors cannot hold a gun to a GM's head. They can only offer her tools of varying usefulness.