I feel like not enough of this thread is dedicated to the fact that Ferio and Clef are apparently sent back on a mission to repopulate Cephiro with each other.
POSSIBLY with Emeraude. I don't know where I stand on her existence as more than a haunting power watching over them at the end. But she's not human anyway? And maybe Eagle but I don't think either of them are going anywhere near him and also I suspect Emeraude has ban-hammered him into another dimension for attempting to end the universe.
Also I'm not convinced Clef is ~human~ in the OVA, never have been. I know he has a priest's robes which echo Zagato's and he calls upon ~the deities~ to help him cast the timewarp
instead of jumping to the left which could be a non-corrupted version of the binding-with-a-creature-and-they-fuel-your-magic variant everyone else seems to mostly have going on (WITH THE EXCEPTION OF EAGLE who is ALSO NOT HUMAN) but his magic seems to operate
entirely differently. So I am more than halfway convinced he's a fae like Emeraude. And Eagle. Maybe. I dunno. It's fun to ponder.
ANYWAY my theory on the actual plot of the OVA goes: someone who likes X:1999 and Rayearth decided to smush them up together~ (like, a distant X fusion, not a crossover, but the undertone is there)
Other theory: OKAY SO the entirety of Eagle's plan is to get a hold of the three deities, who created and are earth. Who are ridiculously powerful. In order to end the universe because the universe has hurt his sister and he will take vengeance for her/the world has proven so unfair and unjust that he wants to start the universe over again, maybe it won't be so terrible next time, either way it'll wipe out all the terrible of this world and all it has done to his sister and all that it has done to him (he is so, so broken) will be DONE.
Or somewhere he thinks that the three gods who are/created earth are a powerful enough force of creation they can restore Cephiro and Zagato. I don't actually think this is what he believes - he seems far too focused on ~burn it all to nothing~ - but I DO think this might be the tale he's poisoning other minds with, the Princess's wish; the way they can undo the wrong done, the way he lured most of the population of Cephiro to their doom. By this point the few he has left are so in his grasp he doesn't necessarily need this promise to control them anyway.
This is based on a theory that the three deities are the ones who created Cephiro, and possibly the entire rest of the universe, before moving on eventually to create and rest as earth. And that legends of them were left behind in Cephiro from when they were there - that to wake them, you need the ones who can SUMMON them, who will appear when their world is in peril to save it.
SO Eagle does the obvious thing: attacks Earth in order to find the three who will wake the gods, and make them do it. (I'm pretty certain he thinks all his minions are expendable and going to die in this effort. It's not like he cares. He's killed everything else already.) And then he will defeat them however he can, and steal their gods, and break all the worlds to nothing so his sister won't hurt anymore.
Not sure if he has a coherent plan of what happens to his sister at that point, possibly she should survive to create a new universe where she will be, in effect, the Pillar - she's more powerful than he is, it's pretty clear, given it's her song he's manipulating to keep people under control - or he's beyond that and just thinks she wants this to be over and to be with Zagato. EITHER WAY ties back neatly to the ending of the first series of Rayearth (for a... given value of neatly).
Clef is a nuisance, because he's taken away the people of Earth, and it would be so much easier to break the girls if Eagle could hurt the people they love. But I don't think he cares too much about that, really. And he can maybe help the girls with magic, but in truth Clef is
only a nuisance. He's not a target, he doesn't matter. Same with Ferio when he defects - Lantis, too, in so many ways, because unless Lantis can actually pull together the strength to murder Eagle (because they both saw their siblings broken by Cephiro and there's such a WEIGHT to their interactions there - I sometimes feel Eagle would let Lantis kill him, because he feels Lantis is the only person with the right to do so - the only other person who is just like Eagle himself, stuck in this because the world destroyed their family - and Lantis can't bring himself to do it, because Eagle won't FIGHT him, and they are the same) then Lantis is not going to stop him from his goal. And that goal is wake the three, get them to fight, and then break them and take their power for his own, for whatever end. (And such an end it would be, a cleansing of everything.)
At the end, when the deities leave, he doesn't stop - he
can't stop - because defeating these three has become his entire goal, defeating them and tearing the universe apart.
When Emeraude says they must start over, he can't accept it - that you can start from somewhere terrible and make something new and strong of it. But that's what the three girls have done - taken a terrible situation and the destruction of their home, and forged a determination and a strength to carry on from it.
AND SO THEN Clef and Ferio are tasked with starting anew in Cephiro and repopulating it!

................................................................maybe with the couple of hundred people I still think Clef had locked away somewhere. But it's less funny that way.