I voted for DND, I see Alpha Flight operating much as Joint Task Force 2 (Canada's Counter Terrorism Unit). Or as part of the RCMP.

Department of National Defence - Official Canada Website
http://www.forces.gc.ca/site/home_e.asp

Department of National Defence (Canada)
http://en.wikipedia.org/wiki/Ministe...e_%28Canada%29

Joint Task Force 2 - Offical Canada Website
http://www.dcds.forces.gc.ca/units/jtf2/default_e.asp

Canadian Special Forces (JTF-2) - Wikipedia
http://en.wikipedia.org/wiki/Joint_Task_Force_2

[RCMP CSIS] Royal Canadian Mounted Police (Div.16) - "Canadian Security Intelligence Service”.
Mandate: Foreign and Domestic Security and Intelligence. (Canada's FBI, CIA, NSA, etc...)

[RCMP SERT] Royal Canadian Mounted Police (Div.17) - "Superhuman Emergency Response Team".
Mandate: Counter Terrorism, Hostage Rescue, and Special Police Services. (Canada's version of SHIELD)

[RCMP PSIS] Royal Canadian Mounted Police (Div.1 - "Paranormal Supernatural Investigation Service". Mandate: Investigate Paranormal, Supernatural, and other Unexplained Phenomena. (Canada's version of SHIELD)

[RCMP AF] Royal Canadian Mounted Police (Div.19) - "Alpha Flight"
Mandate: Superhuman Counter Terrorism, Hostage Rescue, and Special Police Services.


Just a few ideas

QM