tonight on "nightline," vanished, a mystery at 37,000 feet. a jet carrying hundreds of passengers simply drops out of the sky and disappears. tonight an exclusive report, the secrets investigators found buried two and a half miles under the sea. black box mystery, it's supposed to hold the clues to what went wrong. what was the captain doing out of the cockpit in the fury of the storm? why couldn't he save this plane? dangerous skies. with investigators about to issue their final report, what will it tell families about what happened to their loves ones in those last terrifying minutes?

and does it reveal a dangerous problem in the cockpit of our biggest jet? >> good evening. i'm terry moran. it's one of the most astonishing aviation disasters in modern history. air france flight 447 from brazil to paris, vanished three hours into the fight, 228 people lost. flying aboard a state of the art jet, so fool-proof it was called unstallable. so what went so wrong? he's elizabeth vargas with a special "nightline" investigation. >> reporter: it is may 31, 2009, air france flight 447 prepares to depart rio de janeiro.

730, p.m., takeoff it is a routine flight across the atlantic. the plane is filled with vacationers, citizens and families. destination, paris. 8:30 p.m., passengers settle in. there's no sign that one of the biggest mysteries in modern aviation is about to unfold. among the passengers is eth na walls an irish medical students and a riverdance star on holiday in rio. her sister is kathryn. >> her last text was saying she was getting on the flight. she'd had a brilliant holiday. >> reporter: she's on board with 215 other passengers, knowing their lives are in the hands of the men in the cockpit led by captain marc dubois. what they may not know is just how much the captain and his team depend, perhaps disastrously on the sophisticated automated systems

of the plane, the airbus a330, considered to be among the safest in the sky. >> airbus like to say their plane is pilot-proof. >> 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? a minute 30 in 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. the story of flight 447 has ignited a fire storm of controversy about pilot training in the new era of automated flight. >> we're moving towards automated operations where the pilot isn't even permitted to fly. >> reporter: 10:00 p.m., the flight is routine. the crew serves dinner and some passengers settle in to watch an in-flight movie. but 30 minutes later, the plane cruising at 37,000 feet starts to enter a heavy storm system, about 800 miles off the coast of

brazil. instead of flying around the storm, it continues to fly toward it, keeping the automatic pilot system on. was that a bad decision? >> it was certainly a different decision than others took that night. >> reporter: other pilots on the same route choose to fly around the storm. more than 100 miles away from it. >> they were more cautious and did go a bit further away. >> reporter: at the same time, the location of the storm happens to coinside with a known dead zone of radio communication, out of reach of air traffic controllers on either side of the atlantic. 10:35 p.m., the last radio transmission from the air france flight, a routine cowell-out with flight cord nats and then air france 447 vanishes. no one would ever hear from the crew again. it wasn't until 4:41 a.m., six

hours later that french air traffic controllers finally realized something is terribly wrong. by now, friends and family of the passengers are already waiting in the arrival terminal when word began to spread. flight 447 has disappeared. >> this never happens. losing an aircraft is just in itself extraordinary. >> reporter: for hours, french air traffic control tries in vain to locate the a330. no other commercial jet in history has vanished so completely without a witness, without a distress call, without even a trace on the radar. as news of the missing airplane whipped around the globe, now it fell to the crash investigators to solve the mystery. they sent a dozen search and rescue ships to the crash zone. it would take them five days to find anything. by then, much of the wreckage had been disbursed by the ocean's current.

only a fraction was recovered, and just 50 of the 228 people who were on board that night. many were believed to have sunk, still strapped in their seats, along with the plane and the black boxes to the ocean floor, what little rescue crews did find provided a few tantalizing crews. >> we know there was no jurisdiction because or bump because the aircraft was intact at the moment of the crash. >> and there are these clues. no oxygen masks were deployed. there was an empty jump seat with seat belts retracted and a life vest still sealed, floating in its packet. it seemed nobody had prepared for a crash. but without the black boxes, the evidence posed many more questions than it answered. french investigators invested two years and about $50 million trying to find that airplane, all without luck. though finally they called in mike pursel and his team, the same organization that famously found the titanic.

with this underground robot, he coaxed the atlantic to finally give up its secrets. >> we knew immediately that we had found the airplane. >> the robot returned with these photos, parts of the plane fuselage, other small aircraft parts, the galley. they also came back with something else. human remains, definitely put the focus on that this was a real tragedy and a lot of people lost their lives. >> reporter: not only did they find the black boxes in the wrejage, after two years in the water, they still worked. >> reporter: so when you heard what was on the black boxes, were you surprised? when we come back, you'll hear what was happening in the cockpit, the crew in chaos, and where was the pilot as flight 447 was going down? as a culinary manager i make sure our guests

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>> two years after air france flight 447 suddenly disappeared, the plane's black boxes were recovered intact. they hold the clues to the series of unthinkable events that brought down the plane. and for the first time, shed disturbing light on what really happened in the cockpit in the final desperate moments. here against is abc's elizabeth vargas. >> reporter: it is three and a half hours into the flight, almost 11:00 p.m. and the airplane is still cruising at 37,000 feet when captain marc dubois, a veteran air france pilot, makes a fateful decision.

his airbus a330 is heading into a thunderstorm 800 miles off the coast of brazil, he gets up to take a scheduled rest break. he makes his first mistake of the evening when he failed to leave proper instructions to the two ko pilots in charge of the flight. it is only a few minutes later that the plane's pitot tube suddenly fails. this means the automatic pilot system shuts off. it's now 11:10 p.m. now control of the aircraft and the lives of the 228 people on board is in the hands of the least experienced of the three-man crew, cedric bonin. >> and the captain is sitting where i'm sitting now? >> yes. on the left side. >> bill vaz of the flight safety foundation and two test pilots joined us in an a330 simulator to recreate what happened in the final crucial moments. >> the auto pilot disconnects? >> yes. let's see how that looks.

there's a warning. the aircraft is now in my control. i have to fly it manually. >> reporter: all of a sudden the computers are not in charge. cedric bonin, just 32 years old, is. at this point captain bonin makes his first mistake. he should have kept the plane flying. he shouldn't have changed anything, but instead he pulled the nose of the plane up. >> a dramatic pitch up. >> reporter: raising the nose is the wrong thing to do and can cause the airplane to fall out of the sky. it's the most baffling minute of the flight. the plane's stall warning goes off. >> stall, stall. >> reporter: but no one seems to pay any attention. >> stall, stall. >> it sounded for a total of 54 sng seconds, which is a long time.

>> on the black box, bonin says i don't have control of the airplane at all. by now the other co-pilot is calling for the captain. where is he, he asks? is he coming? is he keeps saying, what's happening, they call for the captain six times. >> yeah, yeah. >> where does the captain go, how far away from the cockpit? >> only a few feet away. you can get back in ten seconds. >> reporter: we don't know why, but it took the captain more than a minute to return to the cockpit. two sources tell abc news that he was traveling socially with an off-duty flight attendant. were they together? >> when you are speaking of the private life of the pilot, we are not interested in that. >> reporter: but if the pilot is distracted because he's traveling with somebody, potentially, isn't that part of the investigation? >> i don't think it could be an

explanation of accident. >> reporter: when captain dubois does enter the cockpit, he finds a scene of utter chaos. what's happening? i don't know what's happening, one of the ko pilots answered. what does that tell you about what's going on in that cockpit? >> it seems that the pilot did not understand the situation and were not aware that they had stalled. >> reporter: within seconds, the plane has entered a stall, plummeting at 120 miles an hour, in the dark, belly first, with the nose slight lie up. in the confusion, bonin thinks his instruments are wrong. he asks, am i going down? by now the plane is pitching and shuttering as it falls. >> stall, stall. >> reporter: i got the chance to experience what that felt like in the airbus simulator. now we're going down, right? >> yes. >> stall, stall. >> reporter: in the cockpit, confusion has turned to chaos.

both co-pilots are now trying to fly the plane in opposite directions. >> at a point of exasperation where you actually have discipline breaking down and both pilots trying to fly the aircraft. >> reporter: at what point, at what altitude was this jumbo jet beyond saving? >> this aircraft got into a position where no one had ever designed it to be. realistically, somewhere in the area of 10 to 15,000 feet, they were running out of options. >> reporter: it is too late, but not only the final seconds that the pilot realized the plane is doomed. >> the last words we hear on the voice recorder are from the pilot bonin, what's happening? >> exactly. complete confusion. >> those last words were not released by french investigators and only became public when they were leaked last year.

why did you leave parts out? >> well, you know, you have some personal conversation that is not useful to the accident. >> but it's not personal. >> well, maybe i -- >> reporter: it is decisions like that which have led many people to suspect that french authorities aren't telling the whole story about what happened to flight 447.

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>> the airbus a330 is a plane so hi-tech and automated, human error is all but canceled out, but when computerized controls fail, some pilots lack the instincts or skills to stop the worst from happening. and for air france 447, the question still lingers, who is to blame for the 228 lives lost? once more, here's abc's elizabeth vargas. >> reporter: while there's no question that first officer bonin's decision to tilt the nose of the a330 up was a disastrous one, many experts believe there's more to the story than just incompetence in the cockpit. for example, those tubes that froze over in the storm, there have been 18 similar incidents since 2008. air france had already ordered the pitot tubes to be replaced over time with a better model, but the replacement for this

airplane had not yet arrived before the fatal flight. >> why did the pilots refuse to fly those planes? >> we didn't know if it was just the pitot tube or it caused something else. there's been a big shift in the past few months. you don't hear that now. now -- >> what you hear now is a call for more pilot experience. >> yes. >> reporter: air france was so confident in the design of the airbus, it hadn't prepared its crews for the situation they found themselves in that night. >> no one was trained for high altitude stall recovery in the cockpit. >> reporter: nobody? >> no. >> reporter: why not? >> we've automated the environment and we really haven't revisited the old training. >> reporter: at the heart of this is a heated debate about so-called autimation addiction. pilots overly dependent on the computers flying their planes. >> 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: about 180 victims family members have sued air france and airbus, but airbus defends its claim and their design. what should every person worry about as we get on a jumbo jet today? >> you can't ignore the reality that the system got to be incredibly safe. >> reporter: and yet? >> it reminds us how human we are. the systems change. get over it. autimation is here. fine. how are we going to train people to intervene? >> reporter: the remains of more than 140 victims' bodies were recovered from the ocean. kathryn's sister was not among them. >> we didn't say goodbye. we would just love to see her one more time. >> reporter: what would you say? >> i probably would just give her aug