Bring a large pot of salted water to a boil. Working in batches, add the spinach, chard leaves and kale and cook just until wilted, about 5 minutes. Remove with tongs and transfer to a colander set over a bowl to drain and cool. When cool enough to handle, transfer to a kitchen towel in batches and squeeze out the excess liquid. Chop the greens.
Finely chop the chard stems. Heat the butter in a large pot or Dutch oven over medium heat. Add the chard stems, shallot and thyme sprigs. Cook, stirring, until the vegetables soften, 6 to 8 minutes. Sprinkle in the flour and continue to cook, stirring, until golden, about 2 more minutes. Remove from the heat and slowly whisk in the milk. Return to medium heat; add 2 teaspoons salt, 1/2 teaspoon pepper and a few dashes of hot sauce and cook until thickened slightly, 3 to 5 more minutes.
Discard the thyme and stir the greens into the pot. Cook, stirring, until heated through and coated, about 4 minutes. Remove from the heat and stir in the creme fraiche.
Photograph by Ryan Dausch