They are monitoring the X-Men, whose flight is over the Alps now, and send a kind of UFO to attack the commercial plane! The X-Men jump out of the plane, destroy the UFO and end up going the direct route to the ground.
They are captured, and tried by the Changeling (with evidence from Vanisher, Unus, Blob and Mastermind, who have joined up), and sentenced to death. Meanwhile, we discover Factor Three's plan is to provoke a nuclear war between the East and the West, leaving mutantkind to pick up the pieces (because obviously a radioactive wasteland would be a paradise for mutants?). While Summers will 45 years later be quite keen on the idea of mutant overlords, right now he's not buying it, so the X-Men escape and prepare to stop the Mutant-Master's scheme.
This perhaps marks the formal end of the X-Men's relationship with the military (touched on in earlier issues), as Scott and Bobby go on to a military base, try to explain what's going on, and then after being told to leave, they just start destroying missiles. They never satisfactorily prove that there was a threat. Meanwhile, the others are at a corresponding base in eastern Europe, in a similar runaround. The most interesting part about this is the discovery that Hank speaks Russian.
Turns out that the Mutant-Master isn't really a mutant, but a Sirian. With that revealed, his allies turn against him, and he's defeated, and the Professor and Banshee are freed. That the plan made no sense, rather than being a thing we are just supposed to accept, is a key point of the plot and the thing that changes the mind of Changeling and the others.
Presumably, though, in this time, the suicide (or at least disappearance) of five teenagers from Westchester County, New York was reported by the airliner to the U.S. government. Parents would perhaps have been notified. Not quite as realist as all that, then...