Hi! I hope this hasn't been bothering you for eight days now...

I'm assuming that you're talking about the September Massacres of 1792.

The massacres happened following the invasion of France by Austrian and Prussian forces. The war was a major source of worry, since it threatened both the survival of the revolution and the safety of the citizens of Paris, who had been directly threatened by the Brunswick manifesto in July:

Their said Majesties declare, on their word of honor as emperor and king, that if the chateau of the Tuileries is entered by force or attacked, if the least violence be offered to their Majesties the king, queen, and royal family, and if their safety and their liberty be not immediately assured, they will inflict an ever memorable vengeance by delivering over the city of Paris to military execution and complete destruction, and the rebels guilty of the said outrages to the punishment that they merit. . . .

And since the royal family had been captives since 10 August, the invasion was very much seen as an existential threat to Paris as a whole. There was a fear that counterrevolutionaries in Paris would function as a fifth column within the capital and strike at the seat of revolutionary power. In an attempt to protect Paris, suspected counterrevolutionaries were imprisoned, alongside Swiss soldiers loyal to the royal family, who had been taken prisoner when the monarchy was overthrown.

Throughout the revolution there was a lack of trust in the ability of prisons to contain dangerous individuals, which meant that the prisoners were seen as a very real threat. There was still the fear that they would escape or be freed, and then threaten the security of Paris.

Before it happened, Marat explained in l'Ami du peuple no. 680 that killing the prisoners was not only necessary, but also right. They were traitors, and killing them right away was ”the safest and wisest” alternative. The Swiss soldiers had already been massacred on August 10, while their officers were captured. Since the officers had to be considered guiltier than the rank and file, Marat thought that killing them was even more just. He also worried that traitors in the French government would try to draw out the trials of imprisoned counterrevolutionaries until sympathetic soldiers could march on Paris and free them.

Marat's understanding of events (as he explains it in a month later in the Journal de la République française no. 12) was that the only targets of the massacre were ”great evil-doers and counterrevolutionary traitors”, and anyone else who happened to be in the prisons at the time was spared. So the fact that innocent people or potential revolutionary allies were imprisoned wasn't a problem to Marat, since they were immediately freed. Obviously, Marat's description of the massacre is rosier than the generally accepted version. This overconfidence in the capabilities of revolutionary justice to determine guilt and innocence was very common, and based on people's behaviour during the reign of terror it appears to have been a genuine belief among revolutionaries. So, in my opinion it's likely that Marat actually did believe that only the guilty were hurt.