The easiest way to explain the spiritual underground is to first ask you to imagine the overground - the highly visible and well established network of churches, ministries and institutions that are the face of Christianity to our world.
By contrast, the underground is that hidden space, on the outskirts of Christendom, where unknown, unconventional and unlikely candidates do life together in less-formal structures. Historically, they have been pioneers, who have contended for autheticity, honesty and original thought. This has triggered new ideas and given birth to new initiatives.
Many bible stories show God instigating new stuff on the fringes of the established religious order. For example, John the Baptist!
The underground is not about reaction or resistance to the overground. It is about innovation!