After a season in which he started 13 of 20 games and had a 2–6 record with a 5.12 ERA despite missing nearly four months because of a stress fracture in his right humerus, Loewer was traded along with Adam Eaton and Steve Montgomery from the Phillies to the Padres for Andy Ashby on November 10, 1999.[10] The Padres' expectation for Loewer to become the third starter in its rotation was dashed two months after the trade when he suffered a compound fracture of his left tibia and a dislocated ankle as a result of falling out of a hunting blind in a tree near his home at the time in Eunice, Louisiana on January 2, 2000.[11] He missed the entire season when he underwent surgery on July 18, 2000 to repair a partial rotator cuff tear which he sustained while recovering from his hunting accident injuries.[12]
Loewer was activated from the disabled list and optioned to the Portland Beavers on May 31, 2001.[13] Four days after being recalled from Portland on June 6, 2001,[14] he made his first MLB appearance since September 29, 1999 by allowing six runs and six hits in the first 2+1⁄3 innings of an 8–1 Padres loss to the Seattle Mariners at Safeco Field on June 10.[15] Six days later in a 9–2 defeat to the Mariners at Qualcomm Stadium on June 16, he surrendered six runs, seven hits and both a double in the second inning and a triple in the third to John Olerud who completed his second MLB career cycle later in the game.[16][17] Loewer was optioned back to the Beavers the following day on June 17.[18] He was outrighted to Portland on October 11, 2001.[19] After spending an entire year away from the sport, he signed a minor-league contract with the Padres on December 9, 2002.[20] His contract was purchased by the Padres on May 16, 2003.[21]
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