I can only remember this one scene where there is either an angel/demon on top of the roof of a car that is driving over a bridge toward a city. I believe it had a sword type thing and was trying to attack the people inside the car. Not Legion (2010) or Fallen (2006).
Have you considered one of the Prophecy films?
I don’t think that it is prophecy
“The Prophecy 3: The Ascent” features a Nephilim (half-angel) who is a teenager and came out in 2000 so you could easily have seen it when you say.
https://en.wikipedia.org/wiki/The_Prophecy_3:_The_Ascent
and there’s two more that came out in 2005. it’s worth checking out.
I believe the main character is a teenager.
Is it Mortal Instruments?
http://www.imdb.com/title/tt1538403/combined
No I remember watching it around 2006-2007
I’ll go ahead and watch it then and get back to you when I do.