Part I of this review discussed the similarities between embryogenesis, mammalian adaptions to hypoxia (primarily driven by Hypoxia Inducible Factor-1 [HIF-1]), ischemia-reperfusion injury (and its relationship with reactive oxygen species), hibernation, diving animals, cancer, and sepsis, and focused on the common characteristics that allow cells and organisms to survive in these states. Part II of this review describes techniques by which researchers gain insight into subcellular energetics and identify potential future tools for clinicians. In particular, P31 nuclear magnetic resonance to measure high energy phosphates, serum lactate measurements, the use of near infrared spectroscopy to measure the oxidation state of cytochrome aa3, and the ability of the protoporphyrin IX-triplet state lifetime technique to measure mitochondrial oxygen tension are discussed. Additionally, this review will discuss novel treatment strategies such as hyperbaric oxygen, preconditioning, exercise training, therapeutic gases, as well as inhibitors of HIF-1, HIF prolyl hydroxylase (PHD), and Peroxisome proliferator-activated receptors (PPARs).