Bring a large pot of water to a boil. Add the pasta and cook according to package instructions. Before draining, reserve 1 cup of pasta water.
While the pasta is cooking, heat the olive oil in a pan over medium heat. Add the vegan sausage and crumble with a wooden spoon. Cook until slightly browned (3-5 minutes). Remove the sausage from the pan with a slotted spoon and set aside.
Place the pan back on the stove - there should still be some oil leftover in the pan. Add the shallot, garlic and jalapeño and stir to combine. Add a pinch of salt, pepper and red pepper flakes to the pan and continue to cook, stirring frequently until everything is tender (2-3 minutes).
Add the cooked pasta, pesto, cream cheese and a splash of pasta water to the pan and toss until the cream cheese is smooth and everything is coated evenly. Add the cooked sausage and the spinach to the pan and toss until the spinach is wilted. Taste and adjust salt & pepper as needed. You may need to add more pasta water as you are tossing the pasta.
Serve the pasta with more red pepper flakes and fresh basil.