Rinse wheat berries; put in bowl with enough cool water to cover. Soak for 12 hours in the refrigerator. Drain.
In saucepan, combine wheat berries with white part of the green onions, stock, water, sage, red pepper flakes and salt. Bring to a boil over moderate heat. Lower the heat and simmer, covered, for 40 minutes. Stir in the carrots and lentils and simmer, covered, 10 minutes more or just until the lentils are tender. Remove from the heat, stir in the green onion tops, and let stand for 10 minutes.