After a short stint in the minors in 2000, Nathan spent most of the season in the majors, finishing 5–2 and even hitting two home runs. But he struggled with his control, walking 63 in 93 innings and ending the season with a 5.21 ERA. He was on the disabled list twice: from May 17 to June 6 for right shoulder tendinitis and from July 14 to August 18 for an inflamed right shoulder, necessitating arthroscopic surgery on the afflicted shoulder at the end of the season. Nathan divided 2001 between the AAA Fresno Grizzlies and AA Shreveport both starting and relieving, finishing with a disappointing combined 3–11 record and an ERA over 7. Nathan improved slightly in 2002 to 6–12 with an ERA of over 5 at Fresno, but finally overcame his postsurgical struggles to return to the Giants in September with 3 scoreless innings in relief.