The 9/11 attacks are completely mundane. They take even MJ-12 and its "Report" by surprise because Al-Quaeda's organization as a diffuse terror organization (rather like a Mythos cult) doesn't lend itself to being monitored by the Mi-Go as easily as a conventional military force. In the chaos, the military elements of DG and NRO Delta are caught up in rush to assign personnel to the Afghanistan mission and hunt for Al-Quaeda leaders. Both organizations don't try to interfere with this because they don't want to blow their member's covers in "normal" black operations outfits. 

During the operations in Afghanistan, DG and NRO Delta both encounter a variety of Mythos-related activity. Al-Quaeda and the Taliban *have* been dabbling in certain sorceries. These activities have been kept very very secret from the faithful, but are rationalized as acceptable because the "afriti" are only being used against kuffar infidels. DG and NRO Delta agents out of sheer neccessity during a particular operation with the Northern Alliance
co-operate to destroy a nest of Al-Quaeda cultists summoning That Which Was Not Meant To Exist.

They also discover even more sinister in the wreckage: evidence of correspondence with a known Iraqi intelligence official.

Cell A takes the extreme step of revealing itself to the administration upon reports of this situation. They do not tell their contacts about the post-70's cowboy ops and 90's illegal conspiracy. Only that they were once members of a military intelligence unit that used to deal with such matters. George W. Bush has a very bad reaction to this due to his born-again Christian faith. Evidence of Islamists using literal "Satanic magic" is a nightmare beyond
comprehension. DG is resurrected as a black ops Joint Task Force--Task Force Delta Green--with a secret brief to hunt down any enemy of the United States engaged in paranormal practises. DG just happens to recommend existing cell members as "qualified people in this line of work".

Much to their displeasure, DG is given "help". NRO Delta. George W. Bush was, unlike Clinton, briefed about the existence of MJ-12. He was considered a safe Republican, particularly since he brought on previously-briefed officials from his father's administration who retained their MAJIC clearance. The President told MJ-12 to assist the Al-Quaeda hunt in any way possible. To avoid problems, MJ-12 assigned significant elements of NRO Delta to appease the President's demands until they could figure out how to get the Greys to assist. The result is that TF Delta Green is staffed by members of two old enemies who mutually despise each other...but realize there are good reasons to fight side by side.

As TFDG engages in its "crusade", intelligence analysts puzzle over the meaning of the Iraqi connection. They become even more concerned as they painstakingly trace out efforts by Iraqi academics and front companies engaged in archeological research and relics smuggling. Ominous connections are discovered to the Ba'athist archeology program meant to reflect glory on Saddam Hussein's regime by exavating the ancient civilizations of Sumer and Babylon. Many of these activities center around cultic sites associated with Dagon and Hastur. Two ancient gods mentioned in the spells used by the Al-Quaeda jihadis in Afghanistan. A pattern of activities similar to what veteran DG members from the OSS days were chacterized by the Nazi organization known as the "Karotechia". The first major TFDG operation is planned--Operation SHOTPUT--using a core team of TFDG operatives and a band of Kurdish peshmerga.

There are two survivors. One dies a day after being picked up in the mountains of Northern Iraq. The other babbles what little he remembers before being committed to a VA mental asylum. What they brought back confirms the administration's worst fears.

And, under the pretext of weapons of mass destruction and support for terrorism, the administration invades Iraq.

TFDG does its work quietly amid the chaos. They know their actions have begun a savage civil war, have destabilized the area, have left their nation open to charges of imperialism and arrogance.  They don't care. They can't dare to care about mercy or the morals of torture or international law. They've seen what the Iraqi Ba'athists tried to awake. What the insurgency uses against American forces now. The dread mysteries beyond reality that *cannot* be allowed to be used by Al-Quaeda and their ilk. They order whole villages bombed and have it dismissed as collateral damage. They seize prisoners and whisk them off as ghost detainees...the overt prisoners at Camp X-Ray at Guantanamo being a mere smoke-screen, a lightning rod for media attention to distract from what is truly being detained there.

The War on Terror has only begun.