The ionosphere, or upper atmosphere, was one of the highest zones of a planet's atmosphere, so named because the gas molecules were ionized by solar radiation.
In 1996, Henry Starling entered Earth's upper ionosphere in the timeship Aeon. (VOY: "Future's End, Part II")
In 2367, Lieutenant Paul Hickman's Type 7 shuttlecraft exploded in the lower ionosphere of Tarchannen III when he tried to land the shuttle on the planet surface. (TNG: "Identity Crisis")
Not long after, a shuttlecraft containing William T. Riker and Ambassador Odan was fired upon as it prepared to enter the upper ionosphere of Peliar Zel. (TNG: "The Host")
In 2368, the Tamarians created a particle scattering field over El-Adrel IV's ionosphere, so the USS Enterprise-D would not be able to beam up Jean-Luc Picard. (TNG: "Darmok")
In 2371, the Enterprise-D was unable to scan the surface of Veridian III to locate Captain Jean-Luc Picard with its sensors as the planet's ionosphere created too much interference. (Star Trek Generations)
The ionosphere of the Drayans' crysata moon contains high levels of electrodynamic turbulence, which caused a Type 6 shuttlecraft from the USS Voyager to crash in 2372. (VOY: "Innocence")
In 2375, Captain Kathryn Janeway ordered Voyager into a high orbit above a class 6 gas giant to avoid ionospheric turbulence. (VOY: "Extreme Risk")