Bastilla glorphs along just fine, taking in input through the tubule, hanging a green protein on that input, processing it with instructions from the nucleus, and allowing products and waste to drift on out into the beyond. The nucleus and organelles communicate via the endoplasmic reticulum with special proteins that have unique "shapes". These shapes only fit into certain receptors, and certain of this shapes are specific to Bastilla, of course. Sometimes other organisms communicate with Bastilla by sending their special proteins in through the tubule, which is ordinarily used for incoming food. When Bastilla needs to respond to one of these extra-organism requests the permeable inside cell wall allows those proteins to drift on out just fine.
One day, the nuclear worker RNA gets an incoming work request protein that seems a bit odd. Although the request "shape" fits a receptor site on one of Bastilla's organelles, it did not come from Bastilla's nucleus (wrong identifier sequence), and the organelle at the bottom of the tubule did not tag it with the green protein. This protein message has got into Bastilla by some route other than the tubule. Thousands of generations of evolution have adapted Bastilla's organelles for this sort of nonsense, and the message is ignored. Life continues.
The alien proteins keep arriving. They have been sighted at the nucleus and one or two mitochondria have ignored them as well. All proteins are short-lived, and expire as soon as their task is complete, even those that fail, so there is, as of yet, no corpus to habeas. Although the foreign proteins are not causing any damage yet, the nucleus is concerned about how they are getting in at all. Special receptor only proteins have been deployed to try and capture one of these alien proteins and drag it back in for vivisection, but they have not caught anything yet. The alien protein messages have been sighted mostly in the off hours when Bastilla is mostly idle, living off previously produced ATP and not busy making much of anything.
So, how are these alien proteins getting in despite the one-way membrane? Is some neglectful or malicious organelle or structure in Bastilla connected to the outside world? What gives?
Ed. note: And I did all of this, and the had to go to Wikipedia to get endoplasmic reticulum, since I just couldn't quite remember it. While there I grabbed cytoskeleton and Golgi body. It's been an awful long time since 9th Grade Biology. I'd say it's quite possible some of this stuff has been discovered and/or named since then, in uh 1991 ?
