What is in the USAF manual as the government approved way to engage a (at the time non-hostile) extra-terrestrial spacecraft in the skies over US territory?
I didn’t do Continental Air Defense. But I was involved in doing local combat air defense of our base when deployed.
AFAIK & IIRC there was exactly zero mention of tactics or ROE for extraterrestrial encounters. There certainly was no training for it.
DoD HQ has plans for damn near everything, including something akin to zombie outbreaks. So it’s a good bet there’s some high level policy guidance written someplace about the ET spacecraft scenario.
But out near the tip of the spear I never encountered any. Sorry.
Shoot first, explain to the massive invasion fleet later. 
I’m gonna assume that a “space” ship wouldn’t get low enough into the atmosphere for the USAF to engage them.
“We come in Peace! Shoot to Kill!”
You fool! We can’t make those plans public! THEY’re listening to everything we say!
The Enterprise (no bloody A, B, C or D) had to back off in the 1960s because of that threat.
The Air Force would turn it over to the Navy claiming they arrived over international waters. The Navy would turn it over to the Coast Guard saying it actually was within the territorial limit of the US, and the Coast Guard would turn it over to the civilian authorities claiming there had been no distress call. The civilian authorities would turn it over to INS claiming they were undocumented. INS would claim there weren’t there because the government always denies.
Short answer, the government would deny it, and blame it on sun outages and shortage of rainfall in the rain forest.
The FAA would issue them a citation for failing to file a proper flight plan.
I hear extraterrestrials only fly VFR.
IIRC they concerned over the USAF discovering them and screwing up the timeline, not shooting them down.
What if they arrive when the weather is below VFR flight minimums though? Ah-ha! Now they are screwed. An FAA inspector will meet them at their landing site and issue a huge stack of citations ranging from equipment violations to lack of a current medical certificate that will make your head spin. I wouldn’t be surprised if they found a way to make the pilot do a few days in a local jail until it is all straightened out.
I’m sorry, but that’s classified.
As I recall the Enterprise put a tractor beam on our plane and it broke up in flight. (not that the Mr Lockheed’s Mobile Flying Coffin might not have crashed anyway)
If it’s IFR who’s gonna seem them. Everybody knows they paint their ships with radar absorbing paint. As far as the op question, any pilot seeing them would immediately make a Sergeant Shultz radio call. “I’m just checking in to say I see absolutely nnnnnuthing”.
F-104s were known for being very fast. And looking very fast. Other than that, well, they were fast.
I found the episode Tomorrow is Yesterday on YouTube, in which a U.S. Air Force plane is about to fire at the crippled starship.
But in watching that, I realized the dialogue referring to the old weaponry and avoiding it was — I think — in the movie Star Trek 4, when the cast was flying through the atmosphere in the Klingon ship and chasing the whales George and Gracie.
I would guess, scramble fighters like they would if a civilian aircraft were unresponsive.
offer them a hot beverage.
Bad move if their biology is based on liquid nitrogen. Might be seen as hostile.
The Great Ronaldo was famously guided by astrology during his period in the White House, however, not only had he seen a UFO, but this was one factor in his magnificent obsession with the threat of Alien Invasion. Very probably there are secret executive orders in abeyance for this unlikely eventuality.
( Unlikely because I can think of no good reason why advanced beings would travel light-years in order to wantonly attack the beings of a small planet unimportant to them. )
It would be easy to mock; not so easy to suggest alternatives to countering the Terror from the Skies.
Cites:
As for Ronald Reagan, like Calvin Coolidge, Theodore Roosevelt, and Franklin D. Roosevelt before him, astrology appeared to be tied into life itself, and important decisions required at least a quick glance to the stars. The Philadelphia Inquirer, for example, insisted that “the signing of the U.S. Soviet treaty eliminating medium-range nuclear missiles” had been signed at 1:30 p.m. on December 8, 1987 based on advise from an astrologer. In addition, many papers reported the story that Ronald Reagan had postponed his inauguration 9 minutes as governor of California till 12:10 a.m. on January 2, 1967 based on astrology calculations.
Reagan became noted as being one of the few governors to actually sign astrology legislation when on August 30, 1974, as Governor of California, he signed legislation which became Chapter 583, and added Section 50027 to the government Code, relating to astrology. The legislation removed Sacramento licensed astrologers from the category of fortune tellers, thus allowing them to practice their trade for compensation.
…
On the other hand, Reagan’s last national Security advisor General Colin Powell, had as part of his job to keep “the little green men” references out of Reagan’s speeches. Reagan, as his speeches clearly show, was fond of the 1950 space-invader movie analogy that the world would unit if faced with an extraterrestrial invasion force. Powell feared that if Reagan kept raising the issue people, would actually start to believe aliens were invading.
Sydney Omarr, The Reagans, and Astrology
There might be a deeper reason for Reagan’s apparent interest in the idea of an alien threat. There is an unconfirmed story that before he became Governor of California, Ron and Nancy had a UFO sighting on a highway near Hollywood. The story was broadcast last February on Steve Allen’s radio show over WNEW-AM in New York. The comedian and host commented that a very well known personality in the entertainment industry had confided to him that many years ago, Ron and Nancy were expected to a casual dinner with friends in Hollywood. Except for the Reagans, all the guests had arrived. Ron and Nancy showed up quite upset half an hour later, saying that they had just seen a UFO coming down the coast. No further details were released by Steve Allen.
…
… Reagan upped the stakes again by including the “alien threat” [again], not in a domestic speech but to a full session of the General Assembly of the United Nations. Towards the end of his speech to the Forty-second Session on September 21, 1987, the President said that, "in our obsession with antagonisms of the moment, we often forget how much unites all the members of humanity. Perhaps we need some outside, universal threat to make us recognize this common bond.
“I occasionally think,” continued Reagan, “how quickly our differences worldwide would vanish if we were facing an alien threat from outside this world. And yet, I ask” – here comes the clincher – “is not an alien force ALREADY among us?”
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The fact that there are so many references in important speeches, off-the-cuff remarks, and just plain conversations, means that – for whatever reason or knowledge about deep UFO secrets that he may have as President – Ronald Reagan does think often about the possibility of an alien invasion, and how this event could become a catalyst for world unity. Talking about these UFO secrets, there is also an unconfirmed story of a special story of a special screening in the White House of the movie “ET” at few years ago, with director Steven Spielberg and a few selected guests. Right after the movie, Reagan supposedly turned to Spielberg and whispered something to the effect, “There are only a handful of people who know the truth about this.”
The Shocking Truth: Ronald Reagan’s Obsession With An Alien Invasion — UFO Evidence c. 1988
Actually, were the end of the world near, or Armageddon, or Alien Invasion, most little nations would start rubbing out their enemies next-door and screw co-operation.