2011 Toyota Highlander Limited - 99K miles. My wife was driving the car today and it shut down while she was driving. I instantly thought about the alternator having gone bad based on what she was telling me. I checked the battery and it was completely shot, replaced it, when I hooked it up the alternator whisped a little smoke so I defintely think it needs a new alternator. My question is it has generated a Brake (in red) - Brake Malfunction warning on the small center notification screen above the radio and I cannot get the car to turnover when I have placed the new battery in it. Does anyone have any experience with this issue? I am planning to have the alternator replaced but wanted to know if there is possibly a larger electrical issue. Any advice related to this issue is greatly appreciated.