Malaysian authorities say they haven't found a trace of the 11-year-old Boeing 777 that disappeared over three days ago. Now troubling questions are emerging. How did two passengers board the aircraft... See More
Malaysian authorities say they haven't found a trace of the 11-year-old Boeing 777 that disappeared over three days ago. Now troubling questions are emerging. How did two passengers board the aircraft with stolen passports? Why did five passengers fail to board at all after they checked in? ABC's Elizabeth vargas spent two years on a "Nightline" investigation into an earlier catastrophic crash with eerie similarities. Could that tragedy shed some light on this one? Reporter: More than 72 hours after Malaysia airlines 370 simply vanished from r5idar screens the mystery is only growing. How did the beijing-bound six-hour flight from Kuala Lumpur simply disappear around 40 minutes in, along with 227 passengers and 12 crew members on board? We're unable to determine the cause or the causes of this incident. Most likely it went in the water. Most likely it went in intact. And most likely we are going to find the wreckage in the next few days. Reporter: And while it may seem unprecedented for a modern jet full of passengers to simply vanish mid-flight, it has happened before. Most recently in 2009. What happened to that jumbo jet remained a mystery for more than two years. It is may 31st, 2009. Air France flight 447 prepares to depart Rio de Janeiro. 7:30 P.M., takeoff. It is a routine 11-hour flight across the atlantic. The plane is filled with vacationers, businessmen, and families. Destination? Paris. 8:30 P.M., passengers settle in. There is no sign that one of the biggest mysteries in modern aviation is about to unfold. The airbus a-330, like Boeing's 777 in last weekend's crash, has a strong safety record. Airbus is proud of the fact, they like to say, that their plane is pilotproof. Reporter: That's the good news. Here is the bad news. Is it true that on any given flight the pilots are at the controls only three minutes? Yes. A minute 30 on takeoff and a minute 30 on landing? That's about right. Reporter: It's a cold fact of modern aviation. Planes pretty much fly themselves. While it's not known what happened to Malaysia airlines 370, the story of flight 447 ignited a firestorm of controversy about pilot training in this new era of automated flight. We're moving towards automated operations where the pilot isn't even permitted to fly. Because of this sophistication and the ability of airplanes to fly themselves, they don't have as much opportunity to actually fly the airplane. Reporter: That would have fatal consequences for the final flight of air France 447. At 10:00 P.M. It is still business as usual on that flight. The crew serves dinner. And some passengers watch an in-flight movie. But 30 minutes later the plane cruising at 37,000 feet begins to enter a heavy storm system. At the same time the location of the storm happens to coincide with a known dead zone of radio communication. Out of reach of air traffic controllers on either side of the atlantic. 10:5:00 P. 10:35 P.M. The last radio transmission from air France flight 447. Sometime in the next six hours the airplane would crash into the atlantic soegs. The captain is sitting where I'm sitting right now. Storm on the left side. Reporter: In 2012 bl Voss, then of the flight safety foundation, joined us in an a-330 flight simulator to recreate what happened in the final crucial moments. The autopilot disconnects. The autopilot disconnects. Reporter: We know from cockpit voice recorders that the captain stepped out to take a break when the autopilot suddenly switched off after ice crystals formed on the sensitive tubes on the airplane's wings. There's a warning. The aircraft is now in my control. He should have just kept the plane flying. He shouldn't have changed anything. But instead what did he do? He pulled the nose of the plane up? A fairly dramatic pitch-up. Reporter: Raising the nose of the plane is precisely the wrong thing to do. It can essentially cause the airplane to start falling out of the sky. It is the most baffling and disastrous minute of the flight. Soon the plane's stall warning goes off. Stall, stall. Reporter: But no one seems to pay any attention. Stall, stall. It actually sounded for a total of 54 seconds, which is a lot of time. Reporter: As the stall gets worse the plane becomes harder to fly. On the black box recordings Bo investment N says "I don't have control of the airplane at all." The co-pilot is calling for the captain. Where is he he asks at one point. When captain Dubois does enter the cockpit he finds a scene of utter chaos. The pilot did not understand the situation and they were not aware that it had stalled. Reporter: Within seconds the plane has entered such a deep stall it is plummeting at 120 miles per hour in the dark, belly first. Stall, stall. Reporter: I got the chance to experience what that felt like in the airbus simulator. Stall, stall. Now we're going down, right? Yes. Reporter: Meanwhile, in the cockpit, confusion has turned to chaos. Both co-pilots are now trying to fly the plane in opposite directions. At what point was this jumbo jet beyond saving? Somewhere in the area of 10,000 to 15,000 feet they were really running out of options. Reporter: It is too late. But it is not until the final seconds that the pilots realize the plane is doomed. And the very last words we hear on the cockpit voice recorder are from the pilot bonin, who says, "But what's happening?" Exactly. Just complete confusion. Reporter: It takes hours for French air traffic control to realize something is wrong. Your attention, please. Reporter: By now friends and family of the passengers are already waiting in the arrivals terminal in Paris, when word begins to spread. Flight 447 has simply disappeared. A scene devastatingly similar to the one that played out in beijing early Saturday morning. Nearly three dozen aircraft and 40 ships from ten different countries are now combing the gulf of Thailand, looking for clues. Back in 2009 it took crews five days to begin finding the first pieces of wreckage from the air France flight. French investigators went on to invest two years and $50 million trying to find the rest of the airplane, without luck. So they called in Mike Purcell and his team. The same team that famously found the titanic. Not only did Purcell's team find the black boxes in the wreckage, after two years in the water they still worked. Today in woods hole Purcell told us about the similarities and the differences between the searches for the two airplanes. There are some similarities. People want to know why it happened. I think that the location of this crash is a little bit different from the air France one. So once the underwater search starts I think that it will be pretty easy to find it. Reporter: The final investigation report concluded that the mechanical error was mishandled and misunderstood by the pilots, who in turn caused the plane to crash by their actions. Some lessons for this investigation, as details begin to emerge. But first they must answer the biggest mystery so far. Where is the airplane? For "Nightline" I'm Elizabeth vargas in New York. Mm. Some eerie similarities. Although the two incidents did involve different types of planes as well as different weather conditions.
This transcript has been automatically generated and may not be 100% accurate.