Gilligan warned not everyone would be happy with the show's ending.
"Just the law of averages tells me that a lot of folks will say, 'Nah, that's not what I hoped for. That's not what I saw in my mind's eye.'
"I don't say that because I think it'll be unsatisfying. I think it will be [satisfying] for a large majority of viewers, and that is certainly our intention, but when you make an investment in a television show, you tend to have a proprietary feeling towards it.
"These characters become your characters, and you have hopes and dreams for them. You have expectations for them."
Few details have emerged about the story arc for the show's final season, but Gilligan said splitting it into two parts gave them more time to work on the story.
"It certainly could have been aired as one long block of episodes, but I think the folks that make those decisions - who are at a pay-grade higher than mine - figured it would be better to do two smaller-sized seasons and to take us through the year 2013," he said.
"I'm very happy about that. I like the idea of us being around a couple more years."
Season three of Breaking Bad is currently airing on Four in New Zealand.
Watch the behind-the-scenes clip from season five:
- Herald online