Speaking to Entertainment Weekly, the actress explained that some storylines will be resolved but other questions will be left unanswered.
"Our writers never disappoint with their season finales, and they're true to form this year," she said. "You'll get some pieces to the puzzle, and you'll get some more empty spaces to the puzzle."
Hannigan revealed that Marshall and Lily's "baby talk is back on the table" and added: "I think fans will be really happy because it will be satisfying and frustrating all at the same time, which is what you want out of a season finale. We want it to be really good, but we really want you to want more."
How I Met Your Mother's executive producer Carter Bays has previously suggested that more will be revealed about the mysterious wedding in the finale.
The show, which has already been renewed for two more seasons, airs on Mondays at 8/7c on The CW.