After the battle ended, the three angel-level beings immediately departed, while Raphael quickly tidied up the battlefield-
He mainly finished off the already gravely wounded Saint of the Andariel family, then immediately left those waters.
Immediately afterward, the Lord of Evil Desires took away the Abyss Entrance, leaving only blood-colored seawater and the mutated fish and marine life within it.
Raphael had not yet finished cleaning up. Since this place was far from any church of the Church of the True Gods, the Official Beyonders would not notice anything unusual for a while, giving him plenty of time.
Raphael caught up with the two pirate ships he had let go earlier and dealt with each separately.
He first attacked the Rose School's pirate ship, though his attacks resembled the aftermath of a battle between Saints.
This was meant to create a false impression of how the Rose School's Saint had been killed. Raphael wanted all the Beyonders aboard to realize that Saints had fought fiercely nearby, with the battlefield moving farther and farther from their ship.
He was actually providing them with a cover story. Later, the Rose School's Saints would naturally assume that another Saint had fought fiercely with theirs and ultimately killed their Saint, but had paid a considerable price for victory.
That would explain why everyone aboard had survived.
Since all the Beyonders aboard this ship were already Raphael's marionettes, as long as they did not arouse the Rose School Saints' suspicions at the outset, he could use them to obtain leads on more Saints.
As for the other ship, Raphael made the marionettes reveal their true identities. Some of the leads they provided gave him a surprising suspicion: the faction behind this ship was most likely the Church of Knowledge!
So Raphael simply killed everyone aboard