Johnson was born in Walnut Creek, California, to Carol Hannah and Rollen Charles "Bud" Johnson. By the time he entered Livermore High School, he was a star in baseball and basketball. In 1982, as a senior, he struck out 121 batters in 66 innings, and threw a perfect game in his last high school start. He also played on a Bercovich team that assembled top players from throughout California.

The Diamondbacks traded Johnson to the New York Yankees for Javier Vazquez, Brad Halsey, Dioner Navarro, and cash in January 2005. Johnson pitched Opening Day for the Yankees on April 3, 2005 against the Boston Red Sox. Johnson was inconsistent through 2005, allowing 32 home runs; however, he regained his dominance in late 2005. He was 5-0 against the Yankees' division rival Red Sox and finished the season 17-8 with a 3.79 ERA, and was second in the AL with 211 strikeouts.  In 2005, The Sporting News published an update of their 1999 book Baseball's 100 Greatest Players. Johnson did not make the original edition, but for the 2005 update, with his career totals considerably higher and his 2001 World Championship season taken into account, he was ranked at Number 60.  Johnson was a disappointment in Game 3 of the 2005 Division Series against the Los Angeles Angels of Anaheim, allowing 5 runs on 2 home runs in 3 innings. In Game 5 in Anaheim, Johnson made an effective relief appearance after Mike Mussina gave up 5 runs and 6 hits to give the Angels a 5-2 lead, but the Yankees were unable to come back in the series.  After an inconclusive year in pinstripes, New York fans hoped that Johnson would return to his dominant style in his second Yankee season. Johnson began 2006 well, but then he struggled to find form. In between some impressive performances, he allowed 5 or more runs in 7 of his first 18 starts for the season. Johnson was more effective in the second half. Johnson finished the season with a 17-11 record, a subpar 5.00 ERA with 172 strikeouts. It had been revealed at the end of the 2006 season that a herniated disc in Johnson's back had been stiffening him and it was only in his second to last start of the season that he decided to get it checked. This exposure had caused him to miss his last start of 2006. After being given epidural anesthesia and a few bullpen sessions he was cleared to start in game 3 of the ALDS, however he gave up 5 runs in 5 2/3 innings.

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