By 1969, Japan had advanced quite far in terms of animation. Especially when a studio would put real effort behind a project, such as when Toei Animation released Sora Tobu Yuureisen in July of that year. Known in English as The Flying Phantom Ship or The Flying Ghost Ship, the film is a 60 minute full-color adventure into suspense, conspiracies, and super science with a few important creators involved.
Like most anime of the era, it was an adaptation of a manga. In this case, the 1960 manga of the same name by Shotaro Ishinomori. Ishinomori began his career in the 1950s and was an assistant of Osamu Tezuka's for a time before establishing a name for himself in the 60s and 70s with Cyborg 009, Kikaider, Skull Man (which was a one-shot comic that got heavily reworked into Kamen Rider), and the original Himitsu Sentai Gorenger, the first of the long-running Super Sentai series. The director was Hiroshi Ikeda, who was an anime director in the 60s and 70s, but also had a long career as a show writer as well. It also featured the work of a little-known key animator named Hayao Miyazaki.
The plot itself revolves around Hayato, an adventurous young boy with a loving family who, along with his father, rescues his dad's boss and wife from a car crash and take them to a spooky mansion to avoid the rain. There, they encounter a mysterious skeletal sea captain and his flying dutchman, who's looking for revenge against the people who betrayed him and killed his family.
After being rescued by the authorities, a giant robot attacks the city proclaiming itself to be a golem, the messenger of the Ghost Ship, and destroys large chunks of the city. Hayato's parents are killed in the destruction, but not before his father tells him they're not his real parents.
After a mourning period, Hayato wants revenge, and accidentally uncovers corporate and government conspiracies, underwater bases, a plot to take over the world, giant talking robot crabs, the truth behind the mysterious sea captain and his flying Ghost Ship, and the sinister truth behind soda. Its all very Deus Ex, only wrapped up within the trappings of 60s super science fiction. As a curious footnote, the movie was one of the first anime to be dubbed in Russian and shown in the Soviet Union.
The Flying Phantom Ship is a mix of horror, mad science, secret societies, and a ghost ship that gets into an aerial battle with a giant robot. The robot itself is merely a step on the ever escalating weirdness of the plot, but it shows the capability to fly, smash buildings, fire missiles, and broadcast threats. Its far, far, far from the weirdest thing in the movie (that would be a giant crab trash talking a guy before dissolving him with soda).