My 2006 has 121000 miles and started acting strange in March. I drove it to the dealer and it died. After the dealer ran the diagnostics test they gave the code for "bad cell 5" and "replace battery". The dealer wanted way too much so I had the car towed home and installed a rebuilt battery this week (my car set for almost 2 months). After putting in new battery it wouldn't start due to the 12v battery being dead. So I replaced the 12 v battery and now it still will not start but all of the displays work. I am getting the red triangle, the check engine light and the "exclamation in the car" on the main display. I don't know if this has any bearing on the problem but I did find the dealer had removed one of my spark plugs and left in under the hood. I re-installed it before attempting to start to car. Does anyone have any advice or experience with a problem like this. Also, the water pump that has been recalled is still on my Prius and hasn't been replaced (would this effect the vehicle starting?
Since you replaced the battery, double, then triple check the orange HV battery connector. It is a twist snap and LOCK type connector. It looks like it is on or connected, but not most of the times. This will prevent starting.
No reply from the OP for over a week makes me guess that the orange HV connector was the problem and that he is now up and running. It would have been nice if the OP had of confirmed this for us though.