It kind of makes me sad when I see people who think Kuja really was betraying Zidane and company in Dissidia 012. They’re missing the whole point of the scene and how far Kuja came since the end of FF9. There are quite a few things within the scene that show the truth.
Kuja tries to tell Zidane to “take his companions and go.” If he wanted them there to get hurt, he would have said nothing to warn them and let the scene play out once Kefka arrived with The Emperor and Ultimecia.
When he sees it’s hopeless to extract them from this situation without a fight, he further warns them, “Ready your weapons if you don’t want to die.”
He goes along with Kefka trying to make him say he was leading Zidane into a trap because he knows he still has some hope of helping Zidane and the rest if Kefka’s crew believes he’s on their side. Admitting he’s not won’t do anyone any good and then they’d just try to kill him as well as the others. This leads into the next point.
Kuja shows no prior desire to fight Zidane in 012 and could have let the manikins take over. He chooses instead to insist on taking on Zidane, Squall, and Bartz himself, and more than one scene clearly shows us why. Even aside from Kefka screaming the reason after the fact (“You LET THEM GET AWAY!!!1111"), we see why he did it all the way back in his scene with Cloud. I discussed this in a role-play application I did for Kuja where I was describing his personality in the Dissidia era: “One point Kuja makes in their conversation is that if Cloud doesn’t fight her [Tifa], someone else will, and can Cloud live with the outcome of that? This reflects Kuja’s own behavior later, when he could have stood back and let the manikins fight Zidane, Squall, and Bartz, but chooses instead to fight them himself so that he can throw the fight and let them win and escape. Although he didn’t want to fight Zidane, he knew that if he did, he could control the outcome of the battle, whereas he couldn’t if he just allowed someone else to step in and do it.” The scene with Cloud is vital to understanding Kuja’s behavior later, and it’s meant to be.
Both bad and good characters see that Kuja is good. Kefka knows this; it’s part of why he’s been plotting against him from the beginning of the game. A good one who sees it is Terra. Her special battle line to Kuja is, “Are you hiding your true feelings?” She saw him when he freed her from Kefka’s mind-control, and although he acted very arrogant about it and claimed it was to show his power, she didn’t believe him. If there was any doubt it was just Terra being naive, Dissidia NT made it clear she was right. And Cloud also has an intriguing special battle line for Kuja: “You can still proceed, even with doubts.” He knows Kuja is trying.
I have no doubt that the creators want players to take away that Kuja is a good person. Still flawed, but trying to do the right things, and for the right reasons—no matter what nonsense he may say to the contrary or how bad the scene looks around him. And it will never not be exciting to me that he was given an actual redemption arc instead of just cutting it off with the tragedy of FF9's ending.
(On a lighter note, I’m thoroughly disappointed that so many characters make references to Kuja having something to do with music … but we never get to hear him sing! A tragedy.
Well, at least we get to hear him recite his favorite poem….)