[1] Recorded data showed that the autopilot remained engaged after the lightning strike, contrary to what the pilots had believed, and the nose-up pitch inputs to the flight controls made by the pilots were countered by the autopilot's pitch trim function, which made nose-down inputs to regain the selected altitude of 2,000 feet (610 m).

When the captain flew the Saab 340, he received a training exercise in which a lightning strike caused a generator failure and resulted in the autopilot becoming disengaged.

The weather in Aberdeen was good, but the forecast for Sumburgh called for thunderstorms with rain, snow, hail, and winds of up to 60 knots (110 km/h).

Although the hour-long flight to Sumburgh required 1,826 kilograms of fuel, the pilots opted to fill the tanks in Aberdeen in order to take advantage of lower prices.

[5] As the aircraft turned south, it was struck by lightning, which entered the airframe at the radome directly in front of the cockpit, and exited at the auxiliary power unit (APU) exhaust in the tail.

During this time, the co-pilot declared a mayday, and the air traffic controller offered all options to the crew for an approach or diversion.

Because the autopilot was still engaged, the control forces the commander experienced (opposing his inputs) were higher than usual for a given column displacement, and he identified that the aircraft did not feel normal.

The ground proximity warning system (EGPWS) generated "SINK RATE" and "PULL UP" alarms near the minimum height reached of 1,100 feet (340 m).

[2]: 21–22 Immediately after the lightning strike, the pilots performed nose-up inputs on the flight controls in order to continue the go-around, which along with small increases in engine power caused the aircraft to climb.

However, the autopilot began moving the pitch trim to the nose-down position to maintain the selected altitude of 2,000 feet (610 m), requiring the pilots to pull the control column with a force of 24 pounds (11 kg).

[2]: 24 Eventually the pitch trim stopped close to 9° (out of a maximum of 10°) and Flight 6780 began to descend at a rate of 1,500 feet per minute.

[2]: 24 When the autopilot disengaged, it left the aircraft with pitch trim that was almost fully nose-down and that made the control column ineffective.

Even if the captain pulled the control column with excessive forces and operated the pitch trim switch, the autopilot was designed not to disengage.

The captain felt that the force required on the control column was higher than usual, due to the autopilot opposing his inputs.

However, the autopilot did not disconnect and was attempting to maintain a target altitude of 2,000 ft AMSL by trimming nose-down while the commander was making nose-up pitch inputs.

The autopilot then disengaged due to an ADC fault and this allowed the commander’s nose-up pitch trim inputs to become effective.

[2]: 33 The AAIB also concluded that the greater authority of the pitch trim than the control column during high-speed flight contributed to the accident.

However, the effects of the startle, likely coupled with the pre-startle stress, reduced the PIC’s cognitive frame of mind to make immediate manual inputs, ignoring other control modes.

Of course the alternative hypothesis is that the PIC (thinking that the autopilot had disengaged due to the lightning strike) may have assumed that his manual control system was impaired, and instigated his tunnelling in that direction.