Inspired by the history of Europeans coming to the New World carrying bacteria to which the native inhabitants had little to no immunity, I thought: "What if aliens visiting Earth carried their own sort of infection or infestation, to which we humans had no immunity?" Sort of a War of the Worlds scenario in reverse...
But I'm sure that sort of thing has already been done by someone, aliens carrying virulent disease(s) humans don't carry. So what if the infestation were of nanites--what if nanites become a standard part of healthcare for any advanced technological species? (Just as hand washing and sterilization of medical instruments become standard at a certain point of development--once bacteria are discovered and found to be potentially harmful.) So that nanites are literally crawling all over (and inside) the bodies of high-tech aliens (or perhaps time travelers from Earth's distant future). What if these nanites potentially posed a risk to the human race?
There are a lot of good reasons for an alien to have its body swarming with nanites. The microscopic little robots could clean off dead flakes of skin like mites do for us, but they wouldn't bring some of the common allergic reactions and uncommon diseases mites carry. In fact, the nanites would logically be designed to attack biological forms that are not their host--so they would get rid of mites. They'd also get rid of bacteria. It would be harder for them to help get rid of viruses because most are so small (and I'm assuming a nanite can't be as tiny), but they would do what they could do, perhaps destroying virus-infested cells very early on.
They'd eliminate communicable diseases very nearly entirely. And they'd help with tissue repairs and so forth. Perhaps they'd make it so that an alien who suffered major trauma--say, a gunshot wound to the chest--would fully recover in an hour or two (well, even a day or two would be pretty miraculous). They might go so far as to make an alien virtually immortal.
This is hardly what we'd normally call "infested." Usually that's something we'd reserve for something with negative consequences, like some sort of parasite.
But what if the negative consequences were for creatures like us, twenty-first century humans, who have not been deliberately doused with tiny self-reproducing machines that attack anything other than the host they were designed to protect? Then we'd see the aliens as if they were infested with a disease, since normal contact with one of them would cause these nanites to jump over onto a human body and start to reproduce there, attacking us because we do not match the biological signature of the original host.
When these hypothetical aliens contact one another, the nanites on a particular alien's body intended to be there would always outnumber those that would accidentally cross over from contact with someone else. The ones designed to be on a particular body could have a swarm and hive mentality--effectively collaborating to defend the host and keep any outside nanites from making any trouble.
But we humans, our immune systems are not designed to fight machines. We would have no immunity at all. Casual contact--a handshake, such as in the Star Trek movie "First Contact," would at first seem to have no ill effect at all. But eventually, perhaps in a few days, Dr. Cochrane finds the skin on his hand begins to sluff off...and his arm begins to swell...in a week, the pain is unbearable and is all over his body. In ten days, he is dead...but everyone he touched and everyone who touched him in the meantime is infested by robots that reproduce wherever they are and which attack whatever does not mach their original host. Leaving everyone totally defenseless...
Actually, nice guy aliens who meet us on purpose would either find a way to shut down their own nanites or would refrain from touching us if they were nanite-infested. But what about alien invaders? Will Smith in Independence Day punches an alien in the face...what if he found that within hours his knuckles began to blister...the virtually impossible uploading-of-a-virus-on-a-completely-unknown-computer-system still works, the shields go down, the aliens get blown up. But pilots first, in droves, then every one they know, then probably the entire human race, find themselves dissolved bit by bit by tiny little machines that don't scrub out or bleach out well enough, that radiation can't entirely eliminate, and which aren't even intended to be a weapon. War of the Worlds, in reverse.
The best scenario for this kind of story might be an accidental encounter. Say a crash landing on our planet. Or an alien space vessel sends a mayday and nearby humans (who've never encountered aliens before) fly a spaceship or starship over to help. Neither the humans nor the aliens would know what the disastrous results to humanity will be. The humans because they don't know the aliens carry nanites--and the aliens because they don't realize we humans don't...
(For a 99 cent short story related to this story idea, please follow this No Revolution Too Small Kindle link.)