Set a large pot of water to boil, for the linguine.
In a large, deep-sided sautée pan, heat the olive oil over high heat and add the onions. Once they are sizzling, turn the heat down to medium and sauté them until they just begin to brown.
Add the garlic and cook for another 1-2 minutes, just until the garlic softens.
Add the tomato paste and the oregano and fennel seed. Mix well and bring to a simmer. Let this cook down until it is thick.
Add the crushed tomatoes and the pinch of sugar. Taste it, and add salt if needed. Let this simmer for 10 minutes.
The pasta water should be boiling, so add your linguine.
Turn back to the pan and add the clams to the sauce, mix to combine and cover the pot. Turn the heat up to medium-high and let the clams steam open, about 5 minutes.
After 5 minutes, check to see if most of the clams have opened. Once they have, uncover the pot and turn the heat all the way up to high. You want to steam off as much liquid as you can while the linguine finishes. Shake the pot and stir often to prevent sticking.
Drain the pasta and turn off the heat on the pot. Pick out any clams that have not opened and discard. Now you have a choice: Serve the clams in the shell (be sure to provide a bowl for them!) or pick out the meats. I pick out the meats for all but one clam per diner, and I use that one clam as a garnish.
To serve, toss the linguine with the sauce, top with the chopped parsley and one clam in its shell.