Roast veggies for ratatouille: If you are making the ratatouille, add eggplant, zucchini, bell pepper, and mushrooms to a baking sheet. Toss with 2 tbsp (per original recipe size) olive oil and a pinch of salt and pepper. Place in the oven for 15 minutes.
Prep tomatoes: Meanwhile, cut the tops off the tomatoes and scoop out the flesh. Chop the tops and flesh and set aside to use in the ratatouille.
Sprinkle tomatoes with a pinch of salt and pepper and place on a lined baking sheet.
Cook onions for ratatouille: Heat remaining olive oil in a large pot over medium heat. Add onion and 1/2 the salt (1/4 tsp). Cook, stirring occasionally, until the onion starts to caramelize (about 8-10 minutes).
Roast veggies and tomatoes: After the veggies have roasted for 15 minutes, stir the veggies to prevent sticking. Place back in the oven and add the pan with the tomatoes as well. Roast another 10-15 minutes until the veggies are tender and tomatoes soften (be careful not too overcook the tomatoes or they will be too soft to stuff).
Continue cooking ratatouille: Once the onions start to caramelize, add garlic and stir for 30 seconds. Add tomato paste and the chopped tomato flesh. Scrape the bottom of the pot for any stuck pieces. Cover and reduce heat to maintain a gentle simmer, stirring occasionally.
Once the roasted veggies are soft, add them to the ratatouille pot (do not add the tomatoes). Take the tomatoes out of the oven and set aside while you finish making the ratatouille. Continue simmering the ratatouille for another 5-10 minutes.
Turn off heat and stir in basil, oregano, and red pepper flakes. Taste and add salt as needed.
Stuff tomatoes: Carefully drain any excess liquid from the roasted tomatoes. Stuff with ratatouille and top with cheese. Place back into the oven until cheese melts, about 5 minutes.
Notes
Ratatouille recipe adapted from Cookie and Kate.Vegan Cheese: I used Follow Your Heart Shredded Mozzarella.