Pauly then told Centre that he would prefer to maintain 5,000ft and asked to deviate left of the flight plan course. This request was granted and 250 was handed off to Chicago Centre. Pauly discussed the weather with the Chicago controller and then spoke with another Braniff flight which was at that time climbing out of Omaha for Kansas City. The crew reported light to moderate turbulence and reported that their weather radar showed nothing of significance further south.

Pauly acknowledged and that was the last heard from 250. Shortly afterwards, several people on the ground who had gone outside to view the approaching storm reported seeing 250 flying in clear conditions at about 4,000ft. Witnesses said it seemed to be heading for a light spot in the approaching cloud wall. 250 was lost from view as it passed over a low cloud shelf, but shortly thereafter, witnesses reported seeing a bright flash and a ball of fire falling through the cloud shelf which was 205 spiralling towards the ground, where it impacted killing all aboard. Just moments after the crash, the wind shifted nearly 180 degrees and increased velocity to about 50kts. Rain began to fall and, within minutes, two funnel clouds had formed.

......Examination of the wreckage showed that the starboard wing failed downward while the tail had failed to the left. Both the rudder and elevator had separated from their attachments, having over-travelled in both directions. There was no evidence of structural or system damage nor damage from hail or lightning. The FDR was destroyed in the fire, but the CVR was still readable. The pilots discussed a hole in the line of clouds ahead and then talked about diverting to Pawnee City. About half a minute later, the words "Ease the power back" were heard, followed by the sound of rushing which continued until the end of the tape 25 seconds later. Just prior to the end of the tape, the stall warning horn was heard four times.

Analysis of the CVR showed that the aircraft was travelling at approximately 270kts, it's recommended turbulence penetration speed. It was determined that 250 would have to encounter a gust of at least 140ft/sec. at an upward angle to cause the tailplane to fail. Chicago Centre's radar tape showed an area of heavy rain just north of the area of the accident. The U.S. Weather Bureau analysed the weather in the area and confirmed that strong outflow from the rain cell north of the accident area would cause extreme low-level turbulence. Further analysis showed that 250 would have just passed through a low-level shear zone when the accident happened.