This happens occasionally when Amazon is looking to decommission the physical server your instance is running on. They might be killing the server to replace a failing hardware component or the server might have simply reached its end of life. Either way from what I understand, their process works something like this:
The physical server gets marked as decommissioned so no new instances get launched on it.
If they can (e.g. they're not dealing with a critical hardware failure), Amazon will wait for some period of time to see if the instances running on the server shutdown or reboot on their own (rebooting an EC2 instance usually results in it getting launched on a different physical server).
After that period completes, Amazon will force the remaining instances to reboot moving them to other physical servers.
As a general rule of thumb, due to this and other quirks in the environment, you should treat any individual server running on EC2 as Ephemeral. Any server may reboot or flat out disappear at any time. Accordingly automating deployment with something like chef or puppet, having solid monitoring, and designing your application to work around failure is critical.