There is not room in the hangar bays for all embarked aircraft. In cases of impending hurricanes or other strong weather, if mission permits, the boat makes every effort to avoid the worst of it. If it is likely that severe weather will still be encountered, the air wing can and will be flown off to various bases if they are close enough.
I have been part of this fly off a couple of times, once spending a leisurely three days at Misawa AFB while USS Ranger ran from a hurricane in the western Pacific while enroute to the Philippines.
If no land bases are near enough, then as many aircraft as possible are put in the hangar bay, and remaining flight deck aircraft are subjected to heavy-weather tie-down. That means for expected winds above 60 knots, a minimum of 20 tie-down chains per aircraft are required.
