In popular culture on my Earth-like planet, alien-abduction stories, anal probing and conspiracy-theories are well-known but largley considered by mainstream culture to be delusions or fanciful ideas taken up by the immaginative, the lonely and the desperate.

Tales often have the common feature describing sadistic experiments, transplants eavsdropping on our thoughts and anal probing.

Of course it (mostly) turns out to be true.

One fine day, an alien fleet turns up, takes over all the communication channels, disables the military-infrastructure of the world instantly by computer virus and demands that we surrender on pain of planetary destruction. After brief attempts at negotiation, threats, a few feeble attempts at shows of force, humanity complies.

The aliens land in cities all over the world and demand that everyone submit to one specific test - an anal probe. When asked why, all they will answer is - "It is necessary for the survival of both our species."

What reason could a technologically and militarily superior race have for wanting to probe everyone's anus?

Because humans are really stupid and overestimate the importance of brain because, no surprise, it's their brain who tell them he's the important one.

But there are only 100 millions neurons in brain. 5 time less than in guts.
Aliens know that (that's why they are so advanced) and after doing "catch and release" they concluded they need to do mass check-up on humanity. They are aliens so they have aliens reason to check us.

Some of them may include:

• A gut bacteria that is actually interplanetary threat to any more developed race. Aliens spotted our tries to escape solar system and want to stop humans from making everyone in the galaxy dumb (like we think that brain eating bacteria make us dumber).




• We are showing strange development in the gut region and it may make us go extinct. And for alien we are like white doves at Disneyland.



• Aliens are much more advanced technologically. Their MRI scan is much better when done from inside and the easiest way is through rectum.

It's a large scale health study

Every few years there's another breakthrough in what your gut bacteria say about your health. These aliens have taken this down to a fine art apart from one particular aspect, how to gather and identify the owner of the bacteria in question.

This particular aspect they're still doing the old fashioned way. Somebody once said that the only way to be absolutely sure where the bacteria came from was to take the sample directly, and it stuck.

Now they, as a culture, have become too homogenised. They no longer have the range of diets and environments to maintain the variety of bacteria that humans have. Something is slowly killing them and they've traced it to a lack of certain bacteria in the gut. If they can't get what they need, the next generation may be the last. And as for why it affects human survival? They'll kill us all if we don't cooperate. Corpses don't fight back.

Parasites

The aliens land in cities all over the world and demand that everyone
submit to one specific test - an anal probe. When asked why, all they
will answer is - "It is necessary for the survival of both our
species."

It's a threat

The aliens are saying that if humans don't comply then they will wipe them out.

What they really mean is that they desperately need humanity for their survival.

The aliens are a parasitic race

On their own planet there was a disastrous disease that killed off the hosts of their parasitism. They have been desperately searching the Galaxy for a new victim species.

The best they have come up with is humans but initially the egg implants they made didn't survive.

Over the years they have tested humans as hosts and conducted research . Now they have developed a bacterium that will live in human bowels and make the environment suitable for their eggs and offspring.

This bacterium will allow humans to survive as well but of course they will have to put up with having a gut parasite living inside them for years before it is 'born' and becomes an adult alien.

The test

This is a lie. Now that the research has been done they are ready to implant eggs to start their new generation of parasites. It's not a 'test' it is mass implantation into their new host species.

I'm thinking there are a couple main threats that could potentially wipe out both species (and be solved by anal probes)

1. A disease spreading across the galaxy has devastated the alien species, and due to the genetic similarities between our two species, will likely do the same to us if we become exposed to it.




2. Some third race (potentially either some intergalactic locust or an incredibly aggressive military empire) has been going from world to world wiping out all life. The alien species identifies that they may be susceptible to earth born pathogens from the initial case study of anal probes, and devises a large scale study to cultivate the most deadly pathogens to these species and release them as bioweapons.

In case 1, they may be looking at what bacteria and viruses our body already has defences against- alternatively they may be taking samples of human DNA to reproduce in the lab, and test the disease on.

In case 2, the answer to their problems lies in the wide range of bacteria we have in our guts, viruses etc. Through this large scale study, they hope to get a large sample of microorganisms which they plan to breed and test on test subjects from race #3.

Religion. That's really the easiest answer. Why would someone do something illogical at great personal expense? Because of an illogical motivation like faith guided by religious rules.

The most basic motivation of this kind is some supernatural punishment for not completing certain objectives like following a set of commandments for daily life. In this specific case the aliens belief refusal could perhaps trigger an armageddon like event.

If you want an explanation of why they started with the occasional abduction call it research. They needed to ensure we qualify. Once the clergy was satisfied we did an invasion was launched.

Now for as to what the aliens exactly belief, that's up to you.