The weather becomes unbearably humid and Stanley hears thunder across the lake, near the mountains. He's surprised that he can even see the mountains, as they usually aren't visible through the haze. X-Ray and Zigzag joke about building an ark as a strike of lightning illuminates a rock formation that Stanley thinks looks like a fist making a thumbs-up sign. He thinks of the first Stanley, who said he survived on God's Thumb in the desert. Nobody knows how he did so without water or food. The image of the thumb remains in Stanley's mind, though in his mind, the lightning comes out of the thumb itself as if the thumb truly belongs to God.
Remember that there's been no rain on Green Lake since Sam's death; the storm in the distance near the mountains now acts as a signal that in order to set things right, one must find the rain and the mountains first. This is supported by the existence of God's Thumb there, as well, as that landmark in particular indicates that the divine is also involved in making the mountains a magical place.