- How I Met Your Mother S06E01 – Big Days
- How I Met Your Mother S06E02 – Cleaning House
- How I Met Your Mother S06E03 – Unfinished
- How I Met Your Mother S06E04 – Subway Wars
- How I Met Your Mother S06E05 – Architect of Destruction
- How I Met Your Mother S06E06 – Baby Talk
- How I Met Your Mother S06E07 – Canning Randy
- How I Met Your Mother S06E08 – Natural History
- How I Met Your Mother S06E09 – Glitter
- How I Met Your Mother S06E10 – Blitzgiving
- How I Met Your Mother S06E11 – The Mermaid Theory
- How I Met Your Mother S06E12 – False Positive
- How I Met Your Mother S06E13 – Bad News
- How I Met Your Mother S06E14 – Last Words
- How I Met Your Mother S06E15 – Oh Honey
- How I Met Your Mother S06E16 – Desperation Day
- How I Met Your Mother S06E17 – Garbage Island
- How I Met Your Mother S06E18 – A Change of Heart
- How I Met Your Mother S06E19 – Legendaddy
- How I Met Your Mother S06E20 – The Exploding Meatball Sub
- How I Met Your Mother S06E21 – Hopeless
- How I Met Your Mother S06E22 – The Perfect Cocktail
- How I Met Your Mother S06E23 – Landmarks
- How I Met Your Mother S06E24 – Challenge Accepted
Ted proves a point to the group by calling up his old friend Punchy, which causes him to impulsively show up in New York. Later, he asks Ted to be his best man at the wedding. Seemingly, this is the wedding shown at the beginning of season six, where Ted must give his speech. However, since then, Robin has asked Ted to be her best man whenever she gets married. Ted and the gang have Thanksgiving dinner at Zoey's house, and Ted and Zoey become friends, though they struggle with their feelings for each other.
Meanwhile, Robin gets a new job at World Wide News, reunited with her former annoying co-host, Sandy Rivers.
Marshall suspects that he is the reason Lily can't get pregnant after meeting a fertility doctor who also happens to be Barney's doppelganger. He learns that he is completely fertile and is overjoyed, but moments later receives bad news that his father has died of a heart attack. The gang tries to support Marshall, and Lily tries to help his mom during Marshall's father's funeral, but Marshall becomes preoccupied when he discovers that he has one final voicemail message from him.
Barney calls his mom and tells her that he is finally ready to meet his real dad.
Ted reveals that he is in love with Zoey, but since Zoey is married, he breaks off his friendship with her. Zoey is also in love with Ted, and is getting a divorce from her husband. Since both don't know how the other person feels, Marshall tells each of them about their feelings, and Ted about Zoey's divorce, and they kiss.
This season, Barney meets one of Robin's friends, Nora (Nazanin Boniadi). He likes her right away, although he does not notice it when he tries to sweet-talk her pretending to be a romantic. However, the next day they play laser tag and he begins to like her even more but is reluctant to admit it. He begins dating her when the group (especially Robin) urges him to. Yet, when he actually almost begins to love her, he ends their relationship by lying about his feelings. Barney then wants to fix the relationship, but is too scared to, when he realizes that he does actually want to settle down one day in the future. Barney finally meets his dad (John Lithgow), but is disappointed to see that his dad is not what he expected him to be.
Marshall wants to quit GNB. Lily supports him with that decision, this makes Marshall unemployed. Marshall and Ted decide to help The Arcadian and are against Barney. Finally Ted decides to testify against Zoey's cause and they break up. In the season finale, Lily finds out that she is pregnant. Ted runs into Zoey and she wants to get back together, but Robin and Barney convince Ted not to get back together with her. Barney runs into Nora and asks her for coffee as Robin watches from behind, seemingly appearing as if she has feelings for Barney.
The last scene is of the future wedding, shown in the first episode of the season, and it turns out to be Barney's. This leaves the viewers with one big question: Who is Barney Stinson marrying?