Victoria, who appeared in the final moments of last night's premiere, had previously not been on the show since 2006.
Bays has now told TV Line that the team had been planning to bring back Victoria since she first left.
"There have been a lot of girls," he joked. "But you really could count on one hand the ones that really had this kind of indefinable chemistry with Josh [Radnor], and Ashley's right at the top of that list. There's something about that story and those actors together that first season that really was something special.
"Great other ladies have come and gone in Ted's life, but Victoria was always someone very special. We knew we wanted to see a little more to that story."
Bays also suggested that Victoria will be "part of the endgame of the series" and explained that she will have a big impact on Ted.
"We haven't seen her since she got on that plane to Germany, essentially, and this will sort of be catching up with her, seeing what her life has been about, and seeing how there's a little bit of destiny to the fact that he happens to run into her this particular night," he said.
"She's bringing with her a little bit of wisdom that will become very important to Ted as the season goes on and as the series goes on."
Bays admitted that the reunion is "not all peaches and cream" but explained that Ted will try to make up for cheating on Victoria, saying: "He feels bad about what he did. This episode is him taking steps to right this wrong that now, six years later, maybe doesn't even need to be righted, but that's just what makes him Ted."
He added: "There's a thematic undercurrent that's been slowly emerging on this season about exploring our past and exploring our history... [The characters are] all in a place where they're ready to be grown-ups now, but there's just so much baggage that they're carrying around. We're going to see some faces from the past. Victoria's one of them. The Slutty Pumpkin [is another]. There may be more down the road."
How I Met Your Mother airs on Mondays at 8/7c on CBS.