Ordovician-Silurian Extinction
In the times following the end of the Ordovician era, the CO2 in our atmosphere made a huge drop. This could have had a huge effect on the shallow seas of the time. Another theory as to this mass extinction is a massive ice age. It is possible that ice came so far south that some shallow seas were to cold for the current life, killing off a large number of species.
Theories
CO2 Drop- This could have majorly affected life in shallow seas. Many early organisms needed CO2 to survive, and if they died, it could have caused an entire collapse in the food web. This could have been triggered by volcanic activity as well as other geologic events.
Gamma Ray Burst- Very few scientists agree with this theory. In this particular instance, a hyper nova 6,000 light years away may have released a massive amount of radiation, enough that it could destroy half of our planets' ozone layer in 10 seconds. Although it is possible and certainly would have destroyed life, there is no strong evidence to support this theory.