Cook noodles in a large pot of boiling water until just done, about 8 minutes, or according to package directions. (Remove a noodle with tongs and taste it for doneness.) Drain noodles in a colander and rinse with cold water to stop the cooking. Set aside.
Heat oil over medium-high heat in a large frying pan or a wok. Add onions and mushrooms and cook, stirring occasionally, until onions are well browned, about 10 minutes. Add asparagus and cook, stirring, about 2 minutes longer.
Stir in cooked noodles, tamari, sake and red pepper flakes. Toss with tongs until heated through, 2 to 3 minutes.
Top noodles with sesame oil, cilantro and black pepper. Serve hot.