Pierce squash in several places with a sharp knife. Cook in a microwave oven at full power (100%) until soft when pressed, 12 to 14 minutes, turning squash over after 5 minutes. Cut in half lengthwise and discard seeds. Scoop out tender squash strands and reserve; discard peel.
Meanwhile, in a 10-inch nonstick frying pan (at least 2 in. deep) or a 12-inch nonstick frying pan, stir sesame seeds over medium-high heat until golden, about 2 minutes. Pour from pan.
Rinse asparagus and cut into 2-inch pieces. Combine asparagus with 1/2 cup water in pan and stir often over high heat just until tender-crisp to bite, 3 to 4 minutes. Pour into a colander to drain.
Add olive oil, garlic, ginger, and green onions to pan. Stir over high heat until sizzling, about 30 to 40 seconds. Add asparagus, squash, and bell pepper. Stir gently just until hot, about 3 minutes.
Pour into a bowl; drizzle with sesame oil and sprinkle with sesame seeds. Add salt and pepper to taste.