Spoilers Off for Wild Mass Guessing pages. You have been warned.
Why the Rena were Wiped Out
By the end of the game, the true cause for the catastrophe that motivates Ardo remains an Ambiguous Situation. The implied situation is that humanity became greedy, and tried to forcibly take all of the advancements that the Rena had willingly shared with them, but many of the details are never made fully clear. Given how much of the revolves around Time Travel, I propose that it's actually a case of Stable Time Loop: because Ardo tries to kill humanity to bring back the Rena, someone with time magic in the present sends a message to the past to try and stop him, and humanity of the past decides the best course of action is to wipe Ardo's whole race out just in case any of them become genocidal in the future.