Like I said, it is based off of a visual novel in which you can make key decisions and choose to go down different paths. The normal story is one path, the Tomoyo story is another.
I don't know if that's the best example, seeing that Visual Arts/Key made both and KyoAni made Clannad and the second (better I have been told) version of Kanon. Whatever.
I get it why there's two ovas that has differnt story. well I think the ova 1 which is the23 ep. is for nagisaXtomoya fans while ova 2 is for tomoyoXtomoya fans... but the 1 I really like is the ova 1 ;D