The F-35 Lightning II is a single-seat, single-engine fifth-generation multirole fighter aircraft under development to perform ground attack, reconnaissance, and air defense missions with stealth capability.
Although it was still in development, S.H.I.E.L.D. acquired many of these vehicles, in the B variant (which has STOL capabilities), and used them as one of its primary combat aircraft, prior to the HYDRA Uprising.
The World Security Council sent two F-35s with a nuclear payload to destroy New York City to prevent the Chitauri invasion from spreading during the Battle of New York. Nick Fury, disagreeing with this order, was able to disable one while the other escaped him. Iron Man redirected the bomb of the second into the Sanctuary through a Wormhole to destroy the Chitauri Command Center, ending the Chitauri Invasion.
When Phil Coulson refused to obey the direct order of handing over Ian Quinn for interrogation and transport him to The Fridge, Agents John Garrett and Antoine Triplett were sent in a S.H.I.E.L.D. Jump Jet to reach The Bus with two F-35s escorting them.