It's been years since I finished the game, so I couldn't remember, but according to what I just read, it's unlocked when you finish the "Harboring a Grudge" villain mission. If you've already finished that mission and don't have it, I don't know what to tell you. About all that I can think of is to try playing that mission again and see if it unlocks.

I finished all the hero missions, but now I'm trying to go back and complete all the hero missions 100% before I do the villain missions

If you're talking about freeplay, that may not be possible. You'll probably need things that are unlocked in villain missions, like Penguin's sub, to get everything in freeplay.