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"I'm strictly an ivory-tower person. I can explain things but I can't do things."
- Isaac Asimov

Alien Trojan  
  Malware from another world!  

"On the other hand, they don't know about us and we've gained quite a lot of familiarity with their own technology. We could probably disguise any penetration of their secure systems by using their own techniques, and in this case the natural reaction for them would be to assume it was, in fact, one of those other human groups rather than leap to the conclusion that 'aliens' were trying to invade their systems."
The Shongair

Ground Base Commander Shairez's carefully built remote was deposited on the roof of a coffeehouse in downtown Tehran...

The 802.11 standard wireless connection of the coffeeshop which had been chosen offered broad frequency wireless connections to the internet with potential victims. Even better, it was completely unprotected, without even the standard WAP's 64-hexadecimal key...

For two days, that was all it did-listen, record, and compress, then retransmit daily dumps of all communications in and out of the coffee shop to the stealthed Shongair ship which had deployed it...

From Out of the Dark, by David Webber.
Published by Tor in 2010
Additional resources -

What do you say when you discover alien malware?

"So far as we know, Madam President, we do. But no security is perfect, and this apparently used a Trojan of an entirely novel design. We don't have any idea where it came from, and the penetration itself was an incredibly sophisticated, coordinated attack which included some brute-force key crunching that ...well, let's say no one on our side ever saw coming."

Thanks to William Carroll for this item.

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Additional resources:
  More Ideas and Technology from Out of the Dark
  More Ideas and Technology by David Webber
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