In a medium saucepan, heat the oil over medium heat.: The pan will shimmer slightly when the canola oil is ready, and you may notice a faint aroma of warm oil. Heating the oil first helps create an even cooking surface so the onion and garlic soften rather than stick. You should hear a gentle sizzle when a piece of onion hits the pan, that tells you the temperature is right. If the oil smokes rapidly, the pan is too hot, and you should reduce the heat to avoid a bitter flavor. Wipe the pan dry and start again if the oil smokes excessively, because burnt oil will taint the sauce.
Once hot, add the onion, jalapeno, and garlic, and cook, stirring occasionally, until softened, about 5 minutes.: As these aromatics cook you will see the onion turn translucent and edges go lightly golden, the jalapeño will soften and the raw edge of the garlic will mellow. The sound will shift from pronounced sizzling to a gentler hiss, and the air will fill with the sweet scent of softened onion . Stir occasionally so nothing browns too quickly. If the aromatics start to brown too fast, lower the heat and add a splash of water to cool the pan; overly browned bits can introduce bitterness into the finished sauce.
Transfer the mixture to a blender.: When you move the softened onion , jalapeño , and garlic into the blender, notice their softened texture and fragrant warmth. Transferring while still warm helps the puree become smoother and encourages the flavors to meld. Be careful when blending hot ingredients, venting the lid slightly or covering with a towel to allow steam to escape, otherwise pressure can build. A common mistake is sealing a hot blender tightly and blending at high speed, which can cause steam to force the lid off; vent carefully and pulse first.
Add the tomatoes and their juice, the tomato sauce, chili powder, and chipotle pepper and sauce, and puree.: Pour in the undrained diced tomatoes and the tomato sauce , sprinkle the chili powder , and add the diced chipotle pepper with a teaspoon of its adobo. As you pulse the blender, you will see the mixture go from chunky to velvety, and the aroma will deepen with smokiness from the chipotle pepper . The texture should be smooth but still slightly textured; if it seems too thin, pulse less and leave some body. A pitfall here is overblending until the puree is paper thin; stop when you still have a pleasant mouthfeel.
Return to the saucepan, and bring to a boil over high heat.: Once poured back into the hot pan, the sauce will hiss softly as the steam meets the metal, and a brighter tomato scent will lift. Bringing to a vigorous boil concentrates flavors quickly. Keep an eye on the sauce here because it can bubble up; reduce the heat if it threatens to overflow. Boiling concentrates the liquid, which is essential to concentrate flavors before you reduce to simmer, so resist lowering the heat too quickly.
Reduce the heat to medium-low, and cook, stirring frequently, until reduced to about 2 cups, about 15 minutes.: As the sauce simmers, watch for it to thicken and cling to the spatula, and listen for a soft bubbling sound rather than an energetic roar. The smell should turn deeper, with the chipotle pepper and chili powder melding into a unified, smoky tomato scent. Stirring frequently prevents scorching on the bottom, a problem that can make the sauce taste burnt; use a gentle scraping motion and keep your eye on the reduction. If the sauce thickens too fast or sticks, lower the heat and stir more often.
Season with salt and pepper.: After reduction, sprinkle in the Kosher salt and black pepper , then taste and adjust. Salt brightens the tomatoes and rounds flavors, while the black pepper adds subtle warmth. Allow the sauce to rest a minute then re-taste, because flavors continue to meld after seasoning. A misstep is salting too early; always adjust seasoning at the end so you are responding to the finished concentrate of flavors.
Let cool, then store in airtight container, until ready to use.: As the sauce cools, its aroma will mellow and the texture will become more cohesive. Transfer to a clean airtight jar and chill; the cold sauce will thicken slightly. Stored properly it will last several days in the refrigerator and months in the freezer. Avoid leaving the hot sauce uncovered at room temperature for long periods, because that invites spoilage. Cool quickly by transferring to shallow containers if you plan to refrigerate promptly.