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, ½ teaspoon salt, and ¼ 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 ½ teaspoon salt and ¼ teaspoon pepper and nestle it among the vegetables.
Cover and simmer over medium-low heat until the halibut is opaque throughout and beginning to flake, 10 to 12 minutes.