1. intelligent microscopic life forms that lived symbiotically inside the cells of all living things. When present in sufficient numbers, they could allow their symbiont to detect the pervasive energy field known as the Force.
2. An unnecessary explanation for something best left ambiguous.
With the re-release of The Phantom Menace, I've seen a lot of people dredging up their old issues with the film. Jar-Jar Binks, of course, is a popular target, but I think the issue that really rankles people to this day is the fact that George Lucas took something as mystical and spiritual as the Force and reduced it to (as Robot Chicken joked) "tiny bacteria swimming in your bloodstream" aka midi-chlorians.
Even in the original trilogy, there was always assumed to be some kind of biological component to the Force. It's intimated several times that a big reason Luke has the potential to be strong in the Force is because he's the son of a powerful Jedi. Return of the Jedi made this even clearer by revealing the significance of Leia being Luke's sister. In a way, that biological element has always been present.
However... it seems pretty clear to me that Lucas introduced the midi-chlorians to facilitate a particular plot point. He wanted Qui-Gon Jinn to have conclusive proof that Anakin was not only strong with the Force but had the potential to be greater than all of the Jedi. Thus, not only does he introduce a prophecy about "the one who will bring balance to the Force" he also makes checking for Force potential as easy and mechanical as checking one's sperm count. It's so when the Jedi Council says, "We're not taking this boy," Qui-Gon has a case that's hard to rebut and Lucas needs to make the Jedi Council indisputably wrong.
Or to put it in screenwriting terms - Lucas tells and doesn't show.
In the first trilogy, we SAW Luke's potential as a Jedi, proven in that moment where he opens his mind and makes the impossible shot to destroy the Death Star. The kicker about The Phantom Menace is that young Anakin is already displaying Force-potential through the mere fact he's able to compete in the pod race. There is the "show, don't tell" of that film - the entire set-piece devoted to showing off what Anakin can do! I think every audience member would have accepted Anakin's Force potential based on that sequence alone.
That's why the midi-chlorian thing rankles - it's unnecessary. Lucas already has a way of accomplishing what he needs. Why do we need proof that Anakin isn't the one? Sure, the offspring of Jedi could be biologically predisposed to be Force-sensitive, but surely it's not impossible that one might be born into a family like that which remains unaware of their potential? Making it so iron-clad eliminates the wonder, the hope that all one might need to be a Jedi is to find the way to embrace the Force. That sense of magic is key to the appeal of the first trilogy.
When you explain something, you rob it of its mystique. Isn't the Force more powerful when we don't know where it comes from? Aren't Hannibal Lector and Michael Myers scarier when we don't know their backstories? Why provide answers when ambiguity is more tantilizing?
Not everything needs to be explained. Let the audience infer some things. They need to be able to bring their own magic to the film. This isn't a pass to leave in inexplicable elements. The next time you're writing exposition, or crafting a scene to answer a question you think the audience will have, ask yourself...
"Is this necessary, or is this a midi-chlorian?"
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