The concepts of tumah and taharah are difficult for many people to understand. Physical beings as we are, and especially as many of us understand the germ theory of disease, we would like to understand where tumah comes from and how it spreads in a physical sense. Sometimes the rules make sense - a rishon touches something and makes it a sheni. Sometimes they don't - a sheni touches a liquid and makes it a rishon. Terumah can go to shlishi but chullin only sheni.
The bottom line is that tumah is a spiritual, not physical phenomenon which therefore has rules that physically do not have to make sense. However, there seems to be one rule about tumah that is physical: to remove it one generally requires an immersion in water.
This again leads back to the confusion with the physical. We use water to wash off dirt. We use water to wash off tumah. If it's spiritual, how does a physical solution solve such a problem?
Rav Avraham Kook, ztk"l, on last week's parasha provides a deep answer. He begins by recalling how the Chofetz Chayim, ztk"l, lived such a simple life that people were amazed by his frugality. When asked about it, he noted that travellers rarely take much in the way of luggage along with them (he'd never met my wife's mother!) and he was just a traveller in this world, his true destination being Olam Haba.
Rav Kook notes that water, while in one sense a life-giving fluid, is in other ways totally hostile to the human body. A person cannot live in water. He literally can't breathe it and prolonged immersion would drown him.
From this, the Rav draws his analogy. By immersing in water, a person leaves the comfortable material world he is used to and enters one which more closely resembles the one his soul is currently living in.
Our neshama, after all, being purely spiritual, is immersed in a completely hostile environment here in this physical world. For the soul, it is like a physical body immersed in water. Without the occasional coming up for air, it would totally drown and be extinguished. By entering the mikveh we are reminded of what our soul is going through, the damage the contact with tumah has done to it. This realization plays a role in the removal of the tumah from us. We come up for air, refreshing our physical lives but it is by entering the mikveh that we refresh our soul by isolating it from our usual comfort zones.
This is a lesson well worth remembering. Too often the physicality of our lives overwhelms us. We forget our mission and become comfortable in an environment that is toxic to our true selves. We values our houses, cars and other luxuries. Instead of earning to live, we live to earn.
The mikveh reminds us that what makes us truly what we are is alien to this world and that our real yearning should be to return to our Father in Heaven. Through immersion in the mikveh, the physical ritual provides us with the spiritual help.