Fans were very disappointed with how the CBS show concluded and now Bays said the alternate ending is very different from the one that aired, reported Ace Showbiz.
"16 days ago today we were in the HIMYM edit room, trying to decide between two very different endings. We only shot one script, but through edit room magic we had two possible outcomes for the series," Bays wrote.
"We chose the ending we chose and we stand by it. But we loved the other version too."
He also posted a picture of the DVD box set. A source describes the other version as a "happy ending."
Earlier, a fan named Katie Woods who was outraged with the ending had launched an online petition, asking the show's producers to rewrite and reshoot the ending. The petition has garnered more than 15,000 signs.