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Following what happens in Logan (2017), almost all the mutants are either killed or captured by the government.

In one scene when Logan is putting Charles Xavier to bed,

Xavier: They do not want me, they want you. Oh, yes. That's how fucking stupid they are.They're waiting for you at the Statue Of Liberty.

Logan: Statue of Liberty was a long time ago, Charles! There are no new mutants. You understand? There was not anyone born in the 25 years. Not anywhere.

Xavier: I've always thought... we were part of God's plan.

Logan: Maybe... May be we're God's mistake.
Logan (2017)

indicating that apart from the captive children at the Transigen research, no other mutants exist (expect Logan, Charles and Caliban of course).

And as Jean Grey puts it in X-Men (2000):

Ladies and gentlemen, we are now seeing the beginnings of another stage of human evolution. These mutations manifest at puberty and are often triggered by periods of heightened emotional stress
X-Men (2000)

indicating that some humans are born with the mutant gene.

So what caused the mutant gene to disappear completely from occurring naturally in humans?

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  • Not exactly a dupe, but this question talks about why mutants stopped appearing. Jan 22, 2020 at 18:53
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    I'm assuming the crap they're putting into the water, food and drink is also suppressing the ability of new mutants to manifest their abilities. It's not that they're not being born, it's that mutants are simply leading normal lives.
    – Valorum
    Jan 22, 2020 at 19:05
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    Didn't Alkali-Tansigen put Anti X-Gene chemicals in global food supplies which both killed off pre-existing mutants and eliminated the X-Gene? Jan 23, 2020 at 16:33

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In the movie Logan, there's an expository scene wherein Dr. Zander Rice reveals how Transigen, based on his work, distributed gene therapy through food products to suppress the X-gene in mutants. You can watch the scene in question here. Said exposition is also foreshadowed in the movie when Will Munson tells Logan about how the farms around his residence are owned by a Canewood Beverage and are used to grow a bad-tasting GMO supercorn. On being questioned by Logan as to why people eat it if it tastes bad, Munson reveals that it's not eaten but drunk in the form of corn syrup as said corn syrup is used to sweeten various ready-to-drink packaged beverages on the market. You can watch this scene here.

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