SHIELD Emergency Protocol 193.6 in effect.
Flightdeck
Steve and Bruce are transported via quinjet to what appears to be an aircraft carrier. In actuality it’s a flying Helicarrier, belonging to SHIELD. The landing deck of the helicarrier was recreated on an old landing strip at Albuquerque International Sunport (ABQ).
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Below Decks and Storage Area
After investigating Loki’s scepter, the team realizes that Loki wanted to be captured. The swayed SHIELD agents attack the Helicarrier, and the Hulk gets angry, in a confined space.
While most scenes on the Helicarrier were shot in the Albuquerque soundstages, the fight between the Hulk and Thor was shot inside this DHL facility at the Wilmington Air Park according to Cinefex #130.
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(The Avengers, 2012)