From the little we saw, Xebec was fighting Roger. Garp may or may not have come later(since he was looking for Roger) with them forced to join forces against him, turning it into a 2 vs 1, but ultimately even Sengoku mentions Xebec to be Roger's foe, so I'm pretty certain it'd ultimately be Roger who will overcome him
However I don't think he'd be killed at that point since I don't see Oda portraying Roger as a killer. There is a reason why Xebec's intro in this fb was with Imu, telling him he'd come back, with him mentioned to have broken so many taboos, knowing Imu's existence, GV having disappeared in a similar manner to Lulusia kingdom(act of an ancient weapon) and there were countless CDs on GV, including the HKs and Gorosei, and we know that Imu can use his servants to interfere himself, so I think that either Imu came himself(through the CD portal) to finish Xebec or he took control of one of his servants to do it
If he came himself, it'd even be the perfect moment for Oda to properly show Imu and strenghten his threat lvl for the final war. And obviously he used the ancient weapon because he wanted to erase anything as far as Xebec is concerned, which also explains his anger when looking at Xebec's bloodline(Blackbeard), knowing that he'd most likely try to finish what his dad started