In a large, wide saucepan, heat olive oil on medium heat. Add the onion and cook, stirring regularly, until just beginning to brown, about 5 minutes.
Add the garlic and cook for 1 minute.
Raise the heat to medium-high and add the tomatoes, thyme, lemon zest, lemon juice, capers, and jalapeño peppers. Simmer for 10 minutes, adding a little water if needed to prevent the sauce from getting too dry. Salt and pepper to taste.
Add 1/3 a cup of white wine and 1/4 cup of water. Bring to a simmer.
Place the fillets in the pan on top of the sauce, skin side down, if the fillets are still in their skin. Cover and reduce heat to medium-low. Cook for 5-10 minutes, depending on how thick the cuts of fish are. Poke the fish with a fork and look for doneness. The fish should still be somewhat rare in the middle, but not raw.
Serve immediately, with tomato sauce generously applied.