Circadian Clock During a Flight
When you travel to different time zones, your circadian clock will be off (incorrect). The reason your circadian clock will be off is because your body has adapted to the time zone you are from. When you enter a new time zone, your circadian clock will still be functioning on the old the time zone. If the time zone difference is $\pm 12$ hours, this is a huge adjustment.

However, your body takes inputs from the environment. That is, you may see it is day light when your body is under the impression it is evening. Your circadian clock is controlled by your master clock located in the hypothalamus. As you take in these external inputs that counter your circadian clock, a group of nerve cells called the suprachiasmagic nucleus will slowly make the master clock adjustment [1]. This resetting can take a few days. 


NIH Jet Lag Prevention Guideline


Additionally, there has been a bit of research on exercise reducing jet lag. In a study, researchers test outdoor exercise with flight crew members and found that the group that exercised outdoors had a hastened re synchronization of their circadian clock [2].

Another interesting article is Jet Lag in Athletes.