Update: March 26, 2015: Follow our live coverage of the Germanwings crash here. Read our original report below on the new cockpit door designs was published on March 19, 2014.

In the ongoing saga of missing Malaysia Airlines Flight 370, the notion that something nefarious took place in the cockpit continues to gain traction. If that is what happened aboard the Boeing 777, it could stand on its head many assumptions about aviation security that have been in place since the hijackings of September 11, 2001.

In the days following 9/11, securing the cockpit was the number one priority for the airline industry. Once-flimsy cockpit doors were reinforced with Kevlar so that no one could force their way in with a gun or with sheer brute force. Doors were required to be bolted and locked at all times once the cabin door was shut. Air marshals were posted near the flight deck (to the point where it became a common parlor game to pick out the guard from the rest of the front cabin). Passengers were forbidden to congregate anywhere nearby.

So how could the supposedly secure cockpit factor into the puzzle? The latest revelations from Kuala Lumpur are fueling two lines of inquiry: The first scenario is that hijackers managed to gain access to the cockpit. At that point, either they forced the crew to take the now-well-known series of bizarre moves that sent the plane zig-zagging into the unknown, or they were experienced aviators and executed these moves themselves. That scenario suggests that they would have known when and how to gain access to the flight deck, too.

As many security experts have warned, the cockpit is not 100 percent secure —doors are opened during restroom and meal breaks, and some carriers may have less stringent policies than others on visits from outsiders. And few airlines have installed what would be the most effective protection: A set of double doors that would allow pilots to come in and out of the cockpit but keep it sealed off from the cabin. Boeing and Airbus do offer intruder-proof security gates on planes, but the added weight can be an issue, and many carriers have chosen not to install them.

The second scenario is that one or both of the pilots plotted to take over the plane, knowing they'd be able to get away with it since no could enter the cockpit. That far-out prospect seemed to gain some credence with the discovery today that some files were scrubbed from the captain's homemade flight simulator. This idea has caused some commentators to question whether pilots should be allowed to lock themselves in.

"Perhaps there needs to be way to get back in that door."

John Magaw, the first person to head the nascent TSA in 2001, told CNN that an always-locked cockpit was a concern since the outset. He said he told airlines, "Don't lock those doors so that you can't get in from the outside if something happens, and it fell on deaf ears," alluding to a well-publicized case of pilots who "flew past the airport because they were both asleep." However, some pilots scoffed at the idea that a locked cockpit is a serious concern, noting that planes are programmed to fly safely and even land on autopilot in the unlikely event both pilots nod off.

Former Jetblue CEO and founder David Neeleman, whose airline was the first to install the reinforced cockpit doors system-wide after 9/11, tells PopMech that the latest troubling scenario means that "perhaps there needs to be way to get back in that door."

"But nobody ever thought about having to protect the passengers from the pilots," he says.

Knowledgeable observers caution, however, that nothing incriminatory has turned up yet in the ongoing investigations of the backgrounds of the crew—or, for that matter, the passengers.

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