Sounds to me like a possible fight/commotion in the cockpit was the cause of the plane to fly in such a weird pattern.
Potential Scenario:
- Fight in cockpit results in the plane flying unexpectedly high ("above approved limit")
- Hijackers obtain control, turn off transponder and turn to their target location
- Unexperienced pilot (possibly learned how to only fly smaller planes) makes an "unevenly" descent to lower altitudes as he knows the plane is above its approved limit
- Rise again could be a second fight in the cockpit? Not sure on how to explain this one.
The rising and falling in altitudes makes me suspect this wasn't pilot suicide.