The Shibsa impurity-The reason behind the restrictions prior to washing hands in the morning:
Impurity resides on body: The Sages stated that upon sleeping for sixty breaths at night the G-dly soul of every Jew ascends from the body and a spirit of impurity [which is called Shibsa and Bas Melech] then resides on the body. When the person awakens and the [soul returns to the body] the impurity immediately leaves the entire body and remains only on the hands, until he proceeds to wash them properly. [This spirit of impurity which resides on the hands upon awakening is mentioned both by the Zohar and the Talmud, and due to it, there are restrictions given as to what may be done prior to removing this impurity through washing hands.]
- When at night does the evil spirit reside on the body? Some write that the evil spirit only resides on one’s body if he is sleeping by midnight. Hence if he awoke before midnight or went to sleep after midnight the below mentioned restrictions would not apply. [Divrei Shalom 48, grandson of Rashash in name of Rashash, brought in Kaf Hachaim 4:4 and 52; Shulchan Hatahor 4:10] Practically the Poskim do not differentiate in this matter and the restrictions apply in all cases that one slept at night. [Piskeiy Teshuvos 1:6]
- Other Opinions regarding Ruach Raah: Some rule that today there is no more Ruach Raah and hence one is not required to wash his hands three times in the morning. [See Lechem Mishnah in his explanation of Rambam Hilchos Shevisas Asor 3:2; Rashal in Yam Shel Shlomo Chulin 88; Mahram Chaviv Yuma 44b] Practically, the Poskim above all negate this opinion.
2. How to remove the impurity:
The Talmudic sages stated that the impurity does not [completely] leave ones hands until one pours water on each hand three times. The sages [of Kabala] received a tradition that these three pourings on each hand [must] be done inconsecutively [in order to completely remove all remnant of the impurity from ones hands].
Sparks of Kabala:
The reason why the water has ability to remove the impurity from the hands is because water is Chesed [kindness] while the impurity is Gevuros [severities]. The Chasadim of water thus come and nullify the Gevuros.
 Kama 4:4
Basra 4:2: Upon sleeping the G-dly soul ascends from the body and a spirit of impurity then resides on the body. When the soul returns to the body the impurity leaves the entire body and remains only on the hands.
 Regarding the length of sixty breaths see Chapter 4 Halacha 17 Q&A; Regarding if the spirit of impurity resides even if one sleeps only a temporary sleep see Halacha 6 Q&A.
 Gemara Shabbos 108b; Kaf Hachaim 4:6
 Basra 4:2
 Basra 4:1 and 2
 Siddur; Basra 4:2; Kama 4:4
 Basra 4:2; Tractate Shabbos 109a
 Basra 4:2. This implies that one pouring removes some part of the impurity. [Ketzos Hashulchan 2 footnote 11] Due to this some of the below mentioned restrictions are removed with a single washing. A full three time washing is only required to remove all the impurity and all the restrictions. This will be explained in Halacha 7B in Q&A and Chapter 4 Halacha 12
Other opinions regarding if wiping the hands removes impurity: Some Poskim suggest that perhaps even wiping the hands on an item three times, such as a stone, can remove the impurity. [Birchas Avraham mentioned in Olas Tamid 4:13; Elya Raba 4:12; Kaf Hachaim 4:101]
 Siddur; Shaar Hakavanos of Arizal; Peri Eitz Chaim 3; In Admur Basra 4:2 it is implied that this applies also according to the Sages of the Talmud, although in truth one can read it differently. In Ketzos Hashulchan 2 footnote 11 he writes that according to the Talmud inconsecutive pouring is not needed to remove the impurity. In Kama 4:4 no mention is made regarding who instituted the inconsecutive pouring.
 Siddur and Basra 4:2; Kama 4:4 mentions this as a separate point, without stating that if done consecutively that the impurity will not be removed. Regarding if one may make a blessing if he washed consecutively and no longer has any more water to wash with, see Chapter 4 Halacha 12 with regards to what to do if one does not have enough water.
 Siddur and Basra 4:2; This implies that even consecutive pouring removes some part of the impurity. [Ketzos Hashulchan 2 footnote 11] Due to this, some of the below mentioned restrictions, are removed with a single washing. A full three time inconsecutive washing is only required to remove all the impurity and all the restrictions. This will be explained in Halacha 7B in Q&A; Chapter 4 Halacha 12.
 Kaf Hachaim 4:12