Bring a large pot of water to boil. Add pasta and cook according to the package directions. Drain and set aside.
Heat 1 T. of oil in a skillet over medium heat. Tear up tempeh and add to skillet. Use a wooden spoon to break up tempeh chunks into crumbles. Stir it occasionally for about 10 minutes, until it turns golden brown, then add the pepper fakes, fennel and shoyu. Stir to coat and cook for a few more minutes. Mine always sticks to the pan, and I throw 1/4 cup of water in the pan and swirl it around to scrape all the bits of stuck food from the skillet.
Once the pasta is done, use that pot (or while it’s cooking use a separate saucepan) and heat the other tablespoon of oil over medium. Cook the onion for 10 minutes, until soft and translucent. Add the garlic, thyme and salt, and let cook for one more minute. Stir in the tomatoes, crushing them with the side of the spoon when they get soft. After about 3 minutes, when the tomatoes are starting to break down, pour in the wine. Simmer until the liquid has reduced by half. While it’s cooking, use the back of your wooden spoon to crush the tomatoes on the side of the pan/pot.
When you have a thick, crushed up sauce in the pan, turn off the heat. Stir in the cheese, then the pasta (you may have to rinse it in some hot water if it’s been sitting and all stuck together). Finally, while it’s still warm, stir in the spinach, making sure it gets evenly distributed.
To serve, transfer the pasta to a bowl (they’ll be lots of saucy stuff at the bottom) and top with the tempeh.