Flashforwards on this show are fantastic, granted that they usually end up with a disappointing conclusion (see: the goat). In this flashforward, Ted shows up in a green dress, proudly declaring something to Barney. While it could end up disappointing, this one seems promising.
But back to the show! The Mermaid Theory presents us with three stories. The A story belongs to Ted and the Captain and Ted worries about being killed by him, the B story has Barney and Lily arguing, and the C story focuses on Robin and Marshall testing out the proclaimed titular Mermaid Theory.
The A story, featuring Ted and the Captain, was funny, if a little predictable and been there, done that. The entire story focuses on Ted worrying if the Captain is going to kill him over Zoey, and a majority of the plot focuses on Ted's worried face. It was fun to see Ted so scared, but the show could have done much more with much less; it got a little tiring after a while. The story ended with a nice moment between Ted and Zoey, having a clock begin to count down, implying that sooner or later, Ted will begin to show feelings for Zoey if he doesn't already.
The B story, Barney and Lily's, was frankly a mess. I realize that the purpose was to show how Ted's fading memory results in a messy narrative, and it was a fun thing to experiment with, but the end result was nothing but a confusing mess. First Barney was upset, then we find out it was actually Lily that was upset, then Barney is making beer bottles float in the air, then we find out it was Lily that was upset and she's pregnant. It was a mess of a story, and while it was intentional, it just turned out to be a little confusing.
The C story was interesting. Robin and Marshall are having troubles with conversation, and while it completely lacks continuity, it was a fun little subplot. This is where the Mermaid Theory was truly put to the test, and we find out Marshall is acting so weird because he thinks he will eventually find Robin attractive (but who doesn't?). Seeing Robin in a manatee costume was hilarious, and the ending was kind of cute.
The theme of breaking past barriers was played out in this episode, what with Ted discovering The Captain is not a bad guy and Marshall discovering he will never have feelings for Robin. It was a neat little episode, but some confusing narration by Ted really hurt it from being a classic.