Good question. 1The car broke down on my way here. 2The car had broken down on my way here. 1 would almost always be said in everyday speech. It is simple, and independent. 2 is compound, and dependent. In your context, it would not be said. 2 is a part of something bigger. Eg. 2a"Before they came the car had broken down.", 2b"The car had broken down after they left.", 2c"The car had broken down by then",... Think of it as breaking down at a fixed time (9pm exactly). "had" denotes such a very definite point in time. We get: 2a1: "At 9pm exactly the car had broken down", 2b1: "The car had broken down at 9pm exactly.', 2c1: "The car had broken down at 9pm exactly". Thus "before they came" = "after they left" = "by then" = 9pm.

Present: Sorry I'm late. The car broke down on my way here. Past: Yesterday, my mother was late. The car had broken down on her way here.