This study describes the metabolic, morphologic, neurologic, and functional adaptations observed in the plantar flexors during 8 weeks of lower leg immobilization and 10 weeks of physical therapy following ankle surgery. A combination of magnetic resonance imaging and spectroscopy, isokinetic and isometric muscle testing, and simple functional tests revealed many adaptive changes due to immobilization, including atrophy, loss of muscle strength, reduced central activation, increase in fatigue resistance, and an increase in inorganic phosphate content. After 10 weeks of physical therapy all alterations were reversed, with the exception of a remaining 5.5% deficit in total muscle cross-sectional area.