We find in our sources four different reasons for the obligation to wash one's hands upon waking in the morning.
The Rosh (Rabbenu Asher Ben Yehiel, 1250-1327) writes that the Sages required washing one's hands in the morning because they likely touched the private parts during the night. As the hands became dirty during the night, they must be washed in the morning.
The Rashba (Rav Shlomo Ben Aderet, Spain, 1235-1310) writes that in the morning, Hashem restores our souls which we entrusted to Him when we went to sleep. Not only does He give our souls back – He gives them back to us in perfect condition. We go to sleep tired and worn, and we wake up in the morning refreshed and energized. It behooves us, then, to commit ourselves each morning to pay our debt of gratitude by serving Hashem to the best of our ability. Hence, just as the Kohanim wash their hands before entering the Bet Ha'mikdash to serve, we must similarly wash our hands before we begin our day of devoted service to G-d. According to the Rashba, then, we wash our hands in the morning because we are like the Kohanim, preparing to serve the Almighty.
A third reason appears in the Zohar, which teaches that when a person's soul departs at night, he experiences a kind of death, whereupon harmful spiritual forces overtake his body. These forces leave when one wakes up in the morning, though they remain attached to the hands. We therefore wash our hands each morning to eliminate these harmful spiritual elements.
A similar – but not identical – explanation is given by the Orhot Haim (Rav Aharon Ha'kohen of Lunel, late 13th-early 14th century). Based on the Gemara in Masechet Shabbat (109a), he writes that one's hands become contaminated by harmful spiritual forces overnight, and must be removed by washing. Unlike the Zohar, which speaks of contamination resulting from sleep – a state of quasi-death – the Orhot Haim says that the night itself brings impurity to the hands.
These different explanations will yield practical differences in various situations – such as if one slept during the day, or if one remained awake during the night. We will, please G-d, explore the practical Halachot in subsequent installments.