WARNING: The following article contains spoilers for Marvel's Captain Marvel Prelude #1, by Will Corona Pilgrim and Andrea Di Vito, available now.
Introduced in 2012 in The Avengers, the Quinjet has served as a primary mode of transportation not only for the Marvel Cinematic Universe's premier team of superheroes, but also S.H.I.E.L.D. agents. The Hulk notably left in one of the aircraft at the end of Age of Ultron, and ended up on distant Sakaar, while the fugitive Captain America and his so-called Secret Avengers crisscrossed the globe in another following the events of Civil War, evading detection for two years. Now we have an idea of how.
The newly released Marvel's Captain Marvel Prelude #1, by Will Corona Pilgrim and Andrea Di Vito, traces the footsteps of Nick Fury and Maria Hill between 2015's Age of Ultron and the post-credits scene of this year's Infinity War. Although they (obviously) spent most of that time on the fringes of the MCU, they were nevertheless wired into major events, even if they were occasionally stymied by Stark technology.
As we saw in Thor: Ragnarok, Tony Stark playfully programmed the Avengers Quinjets to recognize team members according to how he viewed them ("Strongest Avenger," "Point Break," and so on). However, some of his modifications were far more practical: As we learn in the canonical Captain Marvel Prelude, Stark's stealth tech prevents the Avengers aircraft from being tracked by S.H.I.E.L.D., or, presumably, by most anyone else.
In the comic, Fury first expresses frustration to Natasha Romanoff following the Hulk's departure, revealing an object was detected in the Banda Sea, in Southeast Asia. "Could be the Quinjet," he concedes, "but with Stark's stealth tech we still can't track the damn thing." The problem, such as it is, seemingly arises again following the events of Civil War, when Hill admits they can't pinpoint the location of the Quinjet commandeered by Steve Rogers and Bucky Barnes. That would help to explain not only how Rogers was able to reach The Raft, the high-security prison in the middle of the Atlantic, but also how Barnes could be transported to Wakanda, where he was granted asylum by King T'Challa, without triggering a diplomatic incident.
That same tech, and presumably that same Quinjet, would permit Steve Rogers, Natasha Romanoff and Sam Wilson, to carry out their mission to take down terrorist cells trafficking in weapons of mass destruction modified with Chitauri technology salvaged from the Battle of New York.
However, Captain Marvel Prelude doesn't wrap up everything in a neat little bow, but instead may introduce a plot hole of its own: After previously communicating with the so-called Secret Avengers through unnamed intermediaries, Fury appears in person, in Syria, to lobby Rogers to bury the hatchet with Stark, leading us to wonder how he found their location.
The other wrinkle is, of course, that if Stark created the stealth tech, then he almost certainly would know how to track it. That would suggest he's known Captain America's every move, from Civil War to Infinity War -- no flip phone required.