Defrag Small Business Server

I’ve got a MS Small Business Server 2003 that recently lost it’s power supply. I replaced the power supply but noticed it seemed to take a really long time to boot up. Ran chkdsk and found three bad clusters. Ran defrag but I’m left with over 50% total fragmented.
Is this an issue with the server not being willing to move a file in use? If so, can I run defrag from a DOS prompt? (It’s NTFS) Or am I looking at a HD that the power supply has damaged?

Thanks,
Paul