The series' creator,
Robert Hewitt Wolfe, was fired after episode 12 of season 2,
Ouroboros (2002), for refusing to dumb the show down enough to suit
Kevin Sorbo, but "his influence was felt until the completion of the second season; at that point, Bob Engels was brought on to be an executive producer." At the time, I boycotted the show after Wolfe's departure, but there were actually some good episodes under Wolfe's departed influence, e.g.
The Knight, Death and the Devil (2002) and
Immaculate Perception (2002).
This episode, however, feels like Wolfe left an intelligent sketch for a season finalé, along the lines of "the first fifty delegates to the restored Commonwealth gather on the Andromeda and Bad Things Happen." The blanks were filled in cluelessly, with the mysterious and inexplicable Alien(s), who at the beginning of the episode, has no problem partially materializing to snatch or kill Commonwealth delegates. It later changes strategy, fully materializing in tactically weak locations to engage in pointless losing hand-to-hand combat.
Then it is reinforced by few enough ships to be defeated by the Commonwealth, followed by a roughly infinite number. Don't expect the idiocy to get an intelligible explanation at the start of season 3; I wasn't able to endure the whole episode, but the reviews here suggest that the new producer didn't even pretend to provide an explanation.