The twist at the end is honestly pretty neat, but this is nothing but twist. I've seen giant bacteria before, and they don't do anything by themselves other than be huge.
I found the concept of a larger Foundation interesting, and giant viruses quite disturbing, yet cool.
+1
Sciencey nitpicks:
Bacteriophages, by definition, infect bacteria, not humans or other multicellular organisms.
I don't think viruses are assigned species.
The message at the end is fun, but I find it hard to believe that you can interpret a foreign language through as high an abstraction as binary code. There are words in the Bible in Ancient Hebrew that we don't know the meaning of, and we can see and read them without decoding! (But if it was just coded English, then nevermind.)
And does the size of the virii mean that the invaders will be made of giant cells? (Cuz that's goofy, and I love it.)
To be honest, besides needing maybe a bit more meat, I think that the on thing holding this back is the inclusion of the bacteria being giant. Obviously they are eventually miniaturized, but I think that them being initially giant is an unnecessary middle-man step.
I think the implication is that they were meant for something quite a bit larger. The problem is the article fails to do anything in that direction so it seems superfluous.
So they're viruses that eat reality-bending powers. Almost feels a little bit too convenient for the Foundation, feels like there should be a catch that would make them have to at least think a little bit about not spraying down every reality bender they find with this stuff and calling it a day.
OOOOH
NOW I GET WHY THEY ARE BIG! Oh god thats gonna be one big monster
I'm fairly sure bacteriophages are viruses, not bacteria.
So this should not be tagged "bacteria" and should instead be tagged "virus".