Sooner or later, you'll be able to attack him. (No spoilers lol)

Keep practicing with your timing and soon you'll get it done.

He will attack you a couple times every round, so you will want to use Refresh, Defense
Up, and Shield as soon as possible. You will probably have to recover HP after every
round, since your attacks won't hit the enemey for now. After a while, you will hear
voices attempting to get through to the masked man. At this point, their attacks will
start to gradually get weaker and weaker. Nonetheless, keep your HP up (use Life Up Beta
and Gamma only) since the boss will try to use PK LOVE against you too.

You just need to keep recovering. Lucas won't attack the Masked Man, but eventually a time
where the Masked Man can be hurt arrives, at which time you don't need to do anything.

It's a bit anti-climactic if you ask me, but it's fine I guess. There's some unused data
that suggests that battle was meant to go on longer, with Lucas actually attacking the
Masked Man, but I doubt we'll actually know anytime soon.

Also, it's suggested that you use Refresh the first turn, recover whenever necessary
(Lifeup Gamma is better than Omega, since it heals what should be about your max health,
while Omega just wastes PP), use PSI Shield and Shield when you can for the first time,
restoring them as they disappear. Also, don't bother trying to revive Duster, Kumatora or
Boney, since the Masked Man will just use a lightning attack, killing them again.

All I do is recover, lol. And you're able to attack the Masked Man after he KOs Flint.

I just let him kill himself.

He kills Flint? I just thought he severely wounded him.

Knock out. Not kill.

And yeah, you can attack him but you don't really get anything from it.