Date: 201409
Local time of day: 1801-2400
Location: ZOA.ARTCC, CA
Flight conditions: IMC
Weather elements / visibility: Thunderstorm
Aircraft: Medium Large Transport; Low Wing; 2 Turbojet Eng
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Flight phase: Cruise
Airspace: Class A ZOA
Reporter organization: Air Carrier
Reporter function: First Officer; Pilot Flying
Second reporter function: Captain; Pilot Not Flying
Anomaly: Deviation - Altitude Excursion From Assigned Altitude; Deviation - Speed All Types; Inflight Event / Encounter Weather / Turbulence
Detector: Person Flight Crew
When detected: In-flight
Result: Flight Crew FLC Overrode Automation; Flight Crew Returned To Clearance
Contributing factors: Weather; Human Factors
Primary problem: Ambiguous

Narrative: This was flight that consisted of three legs with a [late afternoon] show time with 11 hours on duty. During flight preparation and using WSI; weather was noted along most of our route of flight. However; most of the convective activity was North and South of our route. The route was PGUM - IDDAS - YP ... The flight altitude was FL380 and 1700 feet below optimal altitude. As we departed Guam; our flight was given weather deviation to our first waypoint named IDAAS; which is 250 miles from the airport VOR. It is at this point where we will contact ZOA and proceed with Class II navigation operations. The radar was looking actually clear; so the decision was made to ask ZOA for deviations later in the flight; as opposed to just asking GUM center to call ahead for us and give us 30 miles left and right deviation. This I believe was the first mistake that was made in the flight concerning the weather ahead. However; as mentioned before; the radar was showing clear along our route. Over IDAAS is where the second threat took place. The HF radios were not doing well for us on this flight. This would continue to be an issue until we were in contact with MNL radio. With no luck using HF; having tried 4 different frequencies. A few times; we could hear them; but they could not hear us; or the other way around. It was decided that we would use the satellite phone to call ZOA. This however would lead to our second attempt of poor communications with ATC. The first two calls were dropped. The third call was answered and the report was made; however; a request for deviations was not made due again to the radar ahead showing no significant weather along our route; still mainly to the south and north of our course. As we were East of our second waypoint YP; approximately 80 miles. The captain needed to use the restroom; so a call was made to the flight attendants to set up the break. We had discussed needed deviation just prior to YP; and calls were made to ZOA; but again the HF's were just not working with us. As the flight progressed closer to YP; weather had started to build on the radar. The captain again made the call on the phone directly to Oakland Sector ATC for direct communications; and instant deviation approval. However; the call was dropped again. We agreed that we would deviate as necessary to avoid the weather; and it was about this time that the flight attendants called us to notify the cabin was ready for his bathroom break. This was my second error; this was a good time to have both heads in the cockpit; but he needed to use the bathroom. We verified our plan of action; I had my radar on 20 mile scale; and asked him to have his on the 80 mile scale. I had my gain set at two below max intensity and 2 degrees nose down. The seat belt sign had been turned on earlier. At most we expect rain and light turbulence. The captain left and the flight attendant came into the cockpit. I had the oxygen mask on; the cockpit overhead lights were off to aid in seeing the any build ups if possible. However; the moon was not full tonight; so it was a dark night if we were out of the clouds either way. I was already deviating around the weather approximately 4 miles; when a Selcal was received from commercial radio. I answered them on a previously assigned frequency. The communication was 2 by 3 at best. I was however able to request deviations left and right of course 20 miles. The request was received; and in approximately 2 minutes we received the clearance to deviate. Soon after; as I was deviating left of course upwind of the cell about 10 miles; we encountered turbulence; however it was light to moderate at worst with rain showers. We were put into a downdraft that increased our speed. I deselected the auto throttles and reduced power; however the over speed indicator sounded; for about three seconds. As the power was reduced; I was expecting an increase [decrease?] in speed to follow. However; just before this; the stall shaker sounded momentarily. I put the aircraft into CWS B for turbulence penetration. It was at this time that the aircraft lost 700 (seven hundred) feet of altitude. The wings were level at the time of this event; which lasted seconds. Soon after; a climb was initiated back to our cruise altitude. As I was climbing; the Captain called and was ready to come back into the cockpit. As he buckled back into his seat; I debriefed him on what had happened; to include the over speed and shaker. He was surprised and mentioned that in back it just felt as if we encountered light turbulence. We proceeded with our deviations and made an uneventful landing.


Second narrative: We had requested 30 miles deviation to the Left of route for weather. I needed to use the lavatory and left the cockpit. While I was there I felt the turbulence. When I returned to the cockpit the First Officer told me the aircraft lost about 800 feet and that he got the stick shaker twice.


Synopsis: Air carrier flight crew experiences an overspeed then a stick shaker with a 700 foot altitude loss while flying in the vicinity of a thunderstorm at night.