In the 1999 model, the remote batteries have no purpose ither than powering the remote with respect to the power door lock functions. The EIS (electonic ignition switch) does not use any power from the remote. So, changing the batteries will have no effect on a no-start condition.
To begin, try the other keys, including the flat key. If none of the keys work, then you are probably looking at a faulty EIS or other problem. If one of the other keys works, try the failing key again, and if it still does not work, you need a new key.
Other possibilities, if nothing works, include a bad starter.
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