Working on X-Files is how he met Cranston (did a guest spot) and knew he’d be perfect for Walter White even though everybody thought of him as comedic after Malcolm in the Middle. One of those classic lessons for struggling actors on why to do your best every time, 15 years later it can matter.
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One of the episodes Gilligan worked on for X-Files had to do with the Chupacabra and Breaking Bad's Tuco was one of the stars of that.
http://breakingbad.wikia.com/wiki/References_to_The_X-Files
Breaking Bad Wiki
Before creating Breaking Bad, Vince Gilligan regularly wrote episodes for The X-Files. There are a number of small references to The X-Files in Breaking Bad and there are a number of cast members who have appeared in both series.
The cigarette brand smoked by Emilio Koyama and thrown from the RV is "Morley", the same fictional brand smoked by the Cigarette Smoking Man.
The title of the episode "Cancer Man"is a reference to one of the Cigarette Smoking Man's aliases.
Mike Ehrmantraut's surname was used in a Gilligan-penned episode for a minor character.
The time shown on the clock in Gale's Apartment is 10:13. The number 1013 is used frequently in The X-Files as a reference to its creator's birthday.
Dan Wachsberger uses the same bank as Fox Mulder. The van rental company used by Patrick Kuby to rent a van for Walter White is also used in 4 episodes of The X-Files.
When Hank Schrader and Steve Gomez are looking at a bulletin board full of Gustavo Fring's associates in season 5, episode 4 of Breaking Bad, "Fifty-One", the spot where Tuco Salamanca's picture should be is labeled 'Eladio Buente' Eladio Buente is the protagonist of the X-Files Episode "El Mundo Gira", season 4, episode 11. Tuco Salamanca and Eladio Buente were both played by actor Raymond Cruz.
Cast members who have appeared in both Breaking Bad and The X-Files
Bryan Cranston ("Walter White" & "Patrick Garland Crump")
Aaron Paul ("Jesse Pinkman" & "David Winkle")
Dean Norris ("Hank Schrader" & "US Marshal Tapia")
Michael Shamus Wiles ("George Merkert" & "The Black-Haired Man")
Raymond Cruz ("Tuco Salamanca" & "Eladio Buente")
Javier Grajeda ("Juan Bolsa" & "Desk Sergeant")
Danny Trejo ("Tortuga" & "Cesar Ocumpo")
Dale Dickey ("Spooge's Lady" & "Game Warden")
Dan Desmond ("Mr. Gardiner" & "Harry Odell")
John Koyama ("Emilio Koyama" & stunt performer)
Michael Bowen ("Jack Welker" & "Dwight Cooper")