If the battery level goes to low, due to poor planning or an bad weather forecast (winds end up less favorable than forecast) then solar impulse doesn't make it to its destination. If they are over water they crash into the water.
Look, solar impulse is a totally impractical aircraft, built to give the two pilots some records. Everything about the aircraft is impractical and dangerous. There isn't enough power for a decent climb rate or cruise speed. Even a quite common low altitude headwind would be enough to have the aircraft flying backwards. There isn't enough energy storage for sufficient range to safely go any reasonable distance. The structure had to be built extremely light weight so the aircraft is fragile (can't take much turbulence). And there is no way to overcome these limitations with further development.
The maximum solar power reaching earth is about 1kw/sqM, and this is only achieved in clear sky's, when the solar cells are directly facing the sun. Since there is no way to have the solar cells face the sun on an aircraft (the cells have to be flush with the airframe) this means that most of the day you will get even less than 1 kw/sqM (half of the day you will get zero).
To put this in perspective this would mean a light aircraft, like a Cessna 172, would receive a maximum power of 10-15kw of solar energy over the entire airframe. In reality, using very expensive cells with the best efficiency available, the actual energy collected would be more like 3-5kw. A Cessna 172 is a very low powered, low performance aircraft but even still, it gets about 120kw of power from its little 4 cylinder Lycoming engine. The 3-5 kW of electricity that a solar Cessna 172 could collect in the most favorable conditions wouldn't be nearly enough to keep the airplane in the sky. And again, this comparison is not about trying to make a solar powered commuter airliner or something of similar performance, there isn't enough sun for even the lowest performing human carrying aircraft.