In the futuristic world of Logan, the status of mutants is close to non-existent. The only mutants viewers get to see on screen are either working for Transgien or hiding from human civilization about whom they really are. The famous mutant team the X-Men had become nothing more than folklore that is only seen on the pages of comics and the only team members left are older than you last saw them.
Throughout the movie, a mystery builds about why the X-Men disappeared? Donald Pierce had commented that he was responsible for taking down the mutants for Transgien and even Caliban had been a part of the process. An act that seemed to have eaten his soul but he tried to reprimand by helping taking care of Charles.
Charles Xavier at one point or another asks Logan why he was he always was medicated, why he couldn’t remember what happened in the past to a silent Logan who just grunted and never told him why except that he had a brain spasm.
When Charles does suffer from a brain spasm, movie audiences got to witness the altitude of the destruction that it could create. A telepath with a mind control power left unchecked was a safety hazard to all. This energy power suspends everyone and everything in an immediate radius of the Professor, causing the inability to move or even breathe, as well as what looks like an intense headache.
By the time the trio (Logan, X-23, and Professor X) leave in their truck, a radio news broadcaster reports of a similar incident happening only the previous year in Westchester, with 600 people being injured and the death of the X-Men. Charles himself confesses to their murders.
The incident could be the reason why Transgien eradicated every mutant they came across and the reason for the start of the program that created X-23. But the company could have also started the program even without Westchester’s incident. The company is the brainchild of Mister Sinister who, in the comics was obsessed with the manipulation of the mutant gene.