Autumn is beginning to draw in, so military commanders are trying to win a final success before their troops have to go into winter quarters and campainging becomes more difficult due to logisitcal difficulties. Ergo, battles.
I always find it rather unfortunate that Cromwell gets such bad press for the Siege of Drogheda. The practice of killing everyone in cities which refused to surrender when facing overwhelming force was a common one in the era — it held casualties down significantly on both sides if the defenders could be convinced to surrender early. Also, the practicality of army organisation in those days meant that once the disorganised process of taking a city by storm was underway it was very hard to reign in the troops and enforce good discipline; and there's no reason to suppose that the NMA was much better in that regard. If the city had surrendered then Cromwell would have maintained control of his troups the entire time and the outcome would probably have been better than that in many more recent events (such as some in Iraq).
Actually, the NMA might be expected to me worse in that regard to many armies of the era, in that instead of being largely mercenary it was mostly comprised of religious fanatics, and the conflict it was involved in was sectarian.