Zorndyke, a once well-respected scientist, waged war on humanity by melting the polar ice caps and unleashing his army of mutants. Humankind's last hope lies in Blue Fleet, submarines that fight the war. When the question of the war going nuclear becomes apparent, it is up to Hayami Tetsu to find a way to resolve the war without further needless destruction to either side.
Blue Submarine No. 6's main strength lies in its story. Coupled with a potent atmosphere, Blue 6 creates a haunting post-apocalyptic world to use as a backdrop in this war story. Despite this OVA being set around a war, the story benefits more from the parts where there is a lul in the action, allowing the OVA to develop the characters and the world around them.
The characters were as deep as a 4-part OVA would let them be, but Blue 6's length and the shear number of characters naturally resulted in many side characters getting the short end of the stick; besides Hayami, Kino, and a few other major characters, I would be hard-pressed to even remember the names of most of the crew of Blue 6.
I did appreciate Zorndyke's mutant army getting their fare share of screen time. While the commander Verg, a creature whose resemblance to a dog is as great as it is to a human, seemed like precisely the murderous monster humans make Zorndyke's army out to be, you find out that neither he nor anyone else are what they initially seem to be. The most interesting character was Mutio, a fish woman whose life Hayami spared early on. While she was a largely non-speaking character, she probably had the most fascinating development over the course of Blue 6.
While the idea behind Blue 6 was a good one, it was not presented in the best way. I was particularly disappointed in the quality of the visuals. While the traditional hand-drawn cel animation generally looked decent, Blue 6 was perhaps a little too in love with the CG animation, which looked awful. Cowboy Bebop came out the same year as Blue 6 and ostensibly had a smaller per episode budget due to being a 26-episode TV series rather than a 4-part OVA, yet Bebop had CG that looked fantastic and, more importantly, there wasn't the excessive amounts present as there were in Blue 6.
Besides sacrificing time for the characters, it is also because of how poorly animated they were that Blue 6 probably would have benefitted from fewer battle scenes, most of which took place underwater. A lot of the mecha simply didn't look convincing and the overall look of the visuals resembles a video game that came out at around the time this anime was released; the same visuals would've been excellent if they were made for a Nintendo 64 game, not for an OVA.
The sound of Blue 6 did fare a little better than the look. For the most part, the voice acting was very good. I thought Zorndyke's and Hayami's seiyuu stood out the most. The music was made up of pretty catchy jazz pieces. While the ending theme "Minasoko ni Nemure" was a neat jazz song, many of the tunes played during the episodes didn't fit their scenes very well. The scene at the beginning of part 4 in which Verg expresses his frustration to Mutio after she saved Hayami's life comes to mind with this; that scene would have been just fine without any music at all but the jazz playing as Verg shouts with his immense rage was just out of place.
Overall, I would recommend watching Blue Submarine No. 6 for its story and characters, particularly for its fresh take on some themes which can be a little trite, such as "Can't we all just get along?". It is a little disappointing that how Blue 6 was presented was what is keeping it from being a great anime instead of a moderately good one.