Bring a large pot of salted water to a boil and cook the whole wheat noodles according to package directions. Drain and set aside.
Heat 1 tablespoon of olive oil in a large skillet over medium-high heat. Add the shrimp, season lightly with salt and pepper, and cook for 2 minutes per side until pink and opaque. Remove the shrimp to a plate.
Add the remaining tablespoon of olive oil to the same skillet. Stir in the garlic and ginger and cook for 30 seconds until fragrant.
Add the asparagus pieces and cook for 3 to 4 minutes, stirring often, until they turn bright green and stay crisp-tender.
Return the shrimp to the skillet. Pour in the soy sauce and sprinkle the red pepper flakes. Toss everything together for 1 minute so the sauce coats the shrimp and vegetables.
Add the drained noodles and drizzle with sesame oil. Toss well to combine and heat through for another minute.
Remove from heat, sprinkle with sliced green onions, and serve right away.