Entirely independent from S.H.I.E.L.D. and the Alliance, the SCP Foundation is an organization based in the United States dedicated to the research, containment, and secrecy of anomalies. Although they have since been exposed to the public, they still operate, albeit limited.
Relationship with the Alliance
The Foundation had allowed S.H.I.E.L.D. to keep the Alliance, mainly after they were already known to the general public, as they couldn't possibly wipe the minds of entire websites that worship Shrek's left leg. They often tried to edit official documents and news reports to include that they were super soldiers in powered armor, though Shrek would always appear behind them and slap them in the hoohay.
History
Founding
In 1989, a giant tentacle monster attempted to take over the planet. Said monster also shot entire McDonald's buildings out of it's tendrils. After the United States Colonial Marines and the Avengers eventually slapped it's toe and sent it back to the Andromeda Galaxy, mass panic resulted from giant tentacle monsters. Thus, the Foundation was created by one Seagull Joe, a seagull and president of the United States when the actual president wasn't present. They used black magic to erase the memories of the event, though the evidence remained, and did similar things with similar events. They also went to Black Markets to buy strange artifacts that make your hoohay go hoohayhay.
They have since stopped using the dark arts and have opted to not give money to organ stealers, however.
North Korea Incident After an incident involving the Foundation and the Gamers Against Weed, North Korea was nearly wiped off the map after a fifty megaton nuclear warhead that was launched in a last resort attempt to stop an evil clone of Shrek. Afterwards, the Foundation became known to the public after an official announcement from Kim Jong Un.