While still fleeing from Cable and company, Swamp Thing is inadvertently struck by lighting during a strong storm. Matt, Abby, and friend Luke decide to wait the storm but the brash Bolt presses on by himself. A preacher named Father Jonathon Bliss finds and takes Swamp Thing to his church and nurses him back to health. But Bliss' motives are far from altruistic as he is seen speaking to a menacing, odd orb.
Still in search, Bolt is attacked by an unknown object. Meanwhile at the church Swamp Thing helps Father Bliss unblock a passage to a black magic room. There he begins to chant a spell which dulls Swamp Thing's senses so he does not notice the orb seeping away his power, and Swamp Thing falls.
After the rain ceases Matt and Abby continue their search, for Bolt and Swamp Thing. In the search they come across the church of Father Bliss. Suddenly a white-eyed Swamp Thing (Alec is usually red-eyed) bursts forth and attacks them, dragging the trio into the Bliss' lair. There they awaken to see that they are hanging by the hands and that Father Bliss has switched the souls of Alec and the demon inside the orb named Nebiros.
Nebiros, inside Swamp Thing's body, takes Luke, pulls his soul out of his body, and begins to toy and experiment with it. Bliss is horrified by what he sees and Matt begins to talk him out of aiding the demon. When Nebiros finishes with Luke he moves on to Matt but before he can begin, Bliss begins to chant a spell to return Swamp Thing to his original state.
Nebiros is now too powerful and the spell has no effect but the freed Matt destroys the orb releasing Alec's soul and having it drive Nebiros out of his body. In the open and without body Nebiros begins to dissolve. In search of a new one Bliss sacrifices his body so that no one else may be harmed. Once inside Nebiros tries unleash fire, but due to Bliss' weak and frail body the magic is turned unto itself and the Father and demon perish in flames.
In the end Abby, Matt, and Swamp Thing escape the church, and suddenly it crumbles and falls to the ground. While resting outside Swamp Thing notices a helicopter and points it out to Matt. He turns only to find that what he was actually pointing at was Bolt hanging from a line connected to the chopper!