In addition to the reasons we have mentioned, the Chachamim state in the Talmud (Shabbat 108b) that one must be careful that his hands do not touch his mouth, nose, eyes, or ears before washing his hands in the morning because there is a ruach ra’ah (evil spirit) which rests upon one’s hands after sleep and it is likely to damage those organs. Only after he washes his hands three times alternately will the ruach ra’ah disappear and, subsequently, the danger caused by touching any of his bodily orifices will be eliminated.
The essence of the morning washing is to prepare and sanctify oneself for praying Shacharit and for the service of a new day. For that reason, the Chachamim instituted reciting Al netilat yadayim. Nevertheless, we are also careful about the ruach ra’ah, and in order to remove it, we must be strict in washing our hands three times alternately from a vessel. This means that we first wash the right hand, then the left, then again the right and left, and another time right and left, which comes out to be three times, each hand alternately.
Prior to washing, one must take care not to touch those organs that have openings toward the inside of the body – such as the mouth, nose, ears, and eyes (Shulchan Aruch Orach Chaim 4:3-4; Mishnah Berurah 13). Similarly, one must be cautious not to touch food or drink before washing (Mishnah Berurah 4:14).
The Kabbalah teaches (see Zohar, part 1, 184:2) that at night, when a person falls asleep and remains inanimate, without thought and action, he experiences a taste of death and a spirit of impurity (ruach ra’ah) rests upon him. This is in line with Chazal’s statement (Berachot 57b) that sleep is one-sixtieth of death. The essence of human virtue lies in one’s ability to think, feel, and engage in activities leading to the rectification of the world (tikun olam). During sleep, when dormancy spreads throughout the body, a person loses, to a certain extent, the image of God (Tzelem Elokim) within him, and the ruach ra’ah rests upon him. When he awakens from his sleep and his consciousness returns, the ruach ra’ah disappears, remaining solely on the extremities of his hands. By washing one’s hands three times alternately, the ruach ra’ah is removed. In order to completely nullify it, one must begin washing his right hand, which symbolizes the attribute of chesed. Therefore, one should take the washing cup initially in his right hand and pass it over to his left, so that he pours the water over the right hand first and then the left, continuing this way until he has washed each hand three times (see Kaf HaChaim 4:12). In this way, the stern judgments associated with the attribute of gevurah (represented by the left hand) are made subservient to the attribute of chesed (represented by the right hand).
Some explain that the main damage caused by the ruach ra’ah is spiritual; if he were to touch his eyes or ears before washing, his internal senses of sight and hearing would be adversely affected, and on that day he would be like a blind and deaf person concerning matters of Torah and faith. Similarly, if he were to touch his mouth or nose, the ruach ra’ah would harm his spiritual senses of eating and smelling (Kaf HaChaim 4:19, based on Solet Belulah).