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As far as I know, there's no rule that air marshals can only watch suspicious activity. They just did that in this incident to maintain their cover and because this incident never reached the point of an actual hijacking.

"Our FAM agents have to have an event to arrest somebody. Our agents aren't going to deploy until there is an actual event," Adams explained.

The "event" in this case could've been the plane exploding out of the sky, as these men could've gone uninterrupted about the business of assembling a bomb or weapons or whatever. Rest assured the "orthopedic" shoe wasn't checked at the security checkpoint in any way, including for explosives. We might offend someone that way.

http://www.guardian.co.uk/alqaida/story/0,12469,1143626,00.html

Terrorist bid to build bombs in mid-flight

Intelligence reveals dry runs of new threat to blow up airliners

Jason Burke, chief reporter
Sunday February 8, 2004
The Observer

Islamic militants have conducted dry runs of a devastating new style of bombing on aircraft flying to Europe, intelligence sources believe

-snip-

The warning, passed to Western agencies by Middle Eastern intelligence services, is based on interrogations of Islamic militants captured in the Arabian Gulf and is corroborated by intercepted communications between terrorist cells and interviews with prisoners held by the US government at Guantanamo Bay.