He would need to run for Governor again in order to be relevant by 1912.
To my knowledge, TR and Henry Cabot Lodge had planned on building up Roosevelt's political support from 1901-1904 in preparation for a run to succeed McKinley. McKinley didn't seem to have anything against TR, although the Old Guard did, and in fact he did nothing to prevent him from becoming VP in 1900. So it's possible that Roosevelt would be nominated in 1904, though that's far from guaranteed. Fairbanks is likely to be on the 1904 ticket, either as President or as VP.