In Star Trek, a magnetic storm is a spatial phenomenon that posed a navigational hazard in the early days of space travel. At that time, the impulse engines were not powerful enough to resist the effects of such storms, and a ship encountering one could be swept off course. Around 2065, an encounter with a magnetic storm swept the SS Valiant into the galactic barrier initiating a series of events that led to her destruction. (TOS: "Where No Man Has Gone Before")

Magnetic storms can also occur on the surface of some planets. On Rigel XII, they are accompanied by or cause extremely powerful sandstorms. Such a storm nearly claimed the life of Eve McHuron in 2266; only lithium miner Ben Childress' determined search located her. (TOS: "Mudd's Women")

In 2267, the USS Enterprise encountered a magnetic storm at the Halkan homeworld, while James Kirk and his landing party were on the surface conducting negotiations. The storm was reported by Spock to be a "standard ion type, but quite violent and unpredictable." During the beam up to the ship, interference caused by transporting through a magnetic storm caused the crew to transport to an alternate mirror universe. (TOS: "Mirror, Mirror")

While attempting to extract their personnel from the Mokra homeworld in 2372, the USS Voyager hid within a large magnetic storm over the planet's northern magnetic pole to avoid the Mokra's phased ion cannons. (VOY: "Resistance"). In 2373, the shuttlecraft Sacajawea crashed due to a magnetic storm, while attempting to collect nitrogenase compound. Captain Kathryn Janeway was severely injured. (VOY: "Coda").

Such magnetic storms appear to be similar to the real-life phenomena of geomagnetic storms. A geomagnetic storm is a temporary disturbance of the Earth's magnetosphere caused by a disturbance in space weather. Associated with solar coronal mass ejections (CME), coronal holes, or solar flares, a geomagnetic storm is caused by a solar wind shock wave which typically strikes the Earth's magnetic field 24 to 36 hours after the event. This only happens if the shock wave travels in a direction toward Earth. The solar wind pressure on the magnetosphere will increase or decrease depending on the Sun's activity. These solar wind pressure changes modify the electric currents in the ionosphere. Solar wind also carries with it the magnetic field of the Sun. This field will have either a North or South orientation. If the solar wind has energetic bursts, contracting and expanding the magnetosphere, or if the solar wind takes a southward polarization, geomagnetic storms can be expected. The southward field causes magnetic reconnection of the dayside magnetopause, rapidly injecting magnetic and particle energy into the Earth's magnetosphere. Magnetic storms usually last 24 to 48 hours, but some may last for many days.

The largest recorded geomagnetic storm occurred in 1859, when telegraph wires in both the United States and Europe shorted out, some even causing fires. Auroras were seen as far south as Hawaii, Mexico, Cuba, and Italy—phenomena that are usually only seen near the poles. On 13 March 1989 a severe geomagnetic storm caused the collapse of the Hydro-Québec power grid in a matter of seconds as equipment protection relays tripped in a cascading sequence of events. Six million people were left without power for nine hours, with significant economic loss. The storm even caused auroras as far south as Texas. In August that same year, another storm affected microcomputer chips, leading to a halt of all trading on Toronto's stock market.

Intense solar flares release very-high-energy particles that can be as injurious to humans as the low-energy radiation from nuclear blasts. Earth's atmosphere and magnetosphere allow adequate protection at ground level, but astronauts in space elevated radiation and aircraft flying at high altitudes are subject to potentially lethal doses of radiation. The penetration of high-energy particles into living cells can cause chromosome damage, cancer, and a host of other health problems. Ionospheric storms can affect radio communication, navigation systems, satellites and electric power networks.