Heat the oil in a large saucepan over medium. Add the onion and cook for 5–8 minutes until the onion is translucent. Add the garlic and season with salt and pepper. Add the tomato paste and cook, stirring, until color deepens, about 2 minutes.
Stir in the diced tomatoes along with their juices, basil, red pepper flakes, and season with salt. Bring the mixture to a boil, then reduce heat and simmer until sauce is thickened, about 15 minutes.
Add the wine and bring to a boil; cook 2 minutes. Lower heat and bring to a rapid simmer. Add clams and cook until they open, 8–10 minutes. Transfer clams to a large warm bowl; discard any that do not open.
Add mussels and cook until they open, 3–5 minutes. Transfer mussels to bowl with clams; discard any that do not open.
Return sauce to a boil, add shrimp and scallops, cover, and remove from heat. Let sit until shrimp and scallops are cooked through, 5–8 minutes. Transfer shrimp and scallops to another large warm bowl.
Meanwhile, cook the pasta in a large pot of boiling water until al dente, reserving about 1/3 cup of the pasta cooking liquid as needed. Drain the pasta
Return the sauce to a boil. Add pasta and pasta cooking liquid; simmer until sauce thickens, 2–5 minutes and the pasta finishes cooking. Add seafood and continue cooking until well combined, 30–60 seconds. Transfer pasta mixture to a large bowl; season with salt and pepper.