In last night's episode of the CBS sitcom, Marshall (Jason Segel) attended his father's funeral following the character's shock death.
"I started from a place of real sadness [but] I think we struck a good balance of finding humour," Bays told Zap2it.
He added: "The shows we loved [in the past] were shows that were funny 90% of the time. But their humour came from characters and your love of the characters as an audience member. So that 10% when they weren't funny... meant that much more to you."
Bays also confirmed that viewers have not seen the last of Bill Fagerbakke, who played Marshall's father Marvin.
"We'll be able to bring Bill back [in flashback]," he explained. "This won't be the last time we see him on the show."
How I Met Your Mother airs on CBS on Mondays at 8/7c.