Heat the oil in a large skillet over medium heat. Add the onion and cook, stirring occasionally, until soft, 6 to 8 minutes.
Add the squash, garlic, jalapeño, 1/2 teaspoon salt, and 1/4 teaspoon pepper. Cook, stirring occasionally, until the squash begins to soften, 3 to 4 minutes. Stir in the tomatoes and their liquid.
Season the halibut with 1/2 teaspoon salt and 1/4 teaspoon pepper and nestle it in the vegetables. Cover and simmer over medium-low heat until the halibut is opaque throughout and beginning to flake, 10 to 12 minutes.