Well, he was brainwashed and under ultimecia's control..when he was in timber and made contact with edea for the first time form then on he was under her control. even after she was gone from seifer's world, he continued to do as she wanted. After ellone sent ultimecia further into the past in order to acheive time compression, it's not so hard to figure out that she no longer needed seifer to aid her. It's not really hard to figure out what happend, although most of us hate to assume (myself included) it would have most likely went offtrack trying to show you why that happend. On top of that, the 4th disc was mainly dedicated to the cinematic ending.