While reading this comic, keep in mind that neither Mega Man nor X knew where in time the suit had taken them. They were trying to figure it out from the context of what Dr. Light was saying. And if you're wondering why they didn't just ask Dr. Light what year it is, that doesn't work.
Anyway, X's point is that of all the times Dr. Wily has tried to take over the world with eight brand-new robots, only twice has he done so after escaping from prison: the second game and the seventh games. But since Dr. Light didn't use the word "again" to describe Dr. Wily's actions, as X did with Mega Man's in the last panel, we can thus conclude they must be just before the second game. Besides, they're 8-bit, and we all know the seventh game is in 16-bits.
Of course, to someone reading the archives, it might seem pretty obvious that this is prior to the second game, since the rest of the game parodies go in order. But at this point in the comic, there was no reason to believe that. To the readers of the time, this was just some point in the past, and it could've been any of the games.