Actually Pretty Funny: To try and cheer Jean up and snap him out of his funk, Nadia tries to do an impression of a sunny, optimistic Jean by repeating (or rather mangling) his pledge to her back in the Pilot. Jean can't help smiling.
All Myths Are True: Atlantis does exist and did fall in a single day and night. Palto simply lacked more specific details about the fall.
Apocalypse How: The Atlantis of Nadia fell victim to a Class 0, consumed by nuclear weapons fire and infighting.
Atlantis: Ancient Atlantis finally makes its first and only appearance on Nadia.
Clingy McGuffin: Nadia tries to discard the Blue Water into the ocean in the middle of a storm, only for the jewel to come flying back to her. Given the revelations later in the series, it's her Mother's spirit refusing to part from her daughter.
Contrived Coincidence: Played with Eiko having been on the same ship as Jean's Father. On the one hand, it is coincidental, but it also can be justified given the Nautilus' own clashes with the Garfish (and that rescued survivors are recruited into the fight against Gargoyle).
Despair Event Horizon: Jean's Heroic BSoD from the previous episode transitions into this upon receiving confirmation that his father is indeed dead. It takes Nadia to help pull him out of it.
Early-Bird Cameo: A vision of Nadia's Mother (which are implied to be one of Nadia's earliest memories) briefly appears when she tries to throw the Blue Water into the ocean.
Early-Installment Weirdness: Nadia's Mother's character model is different from its subsequent appearances (from the Blue Water's necklace to her facial structure and even clothing).
The vision of a woman appearing when Nadia tries to discard the Blue Water. We'll eventually find out its her Mother (and that her soul is contained within Nadia's Blue Water).
Jean's test on the Blue Water. The strange markings as viewed through the microscope (which we've seen here and there) are advanced electronic circuits (though Jean doesn't have the technological context to recognize that). That, combined with the Blue Water's being able to cut through a piece of Nautilus hull is another clue it's origin is not of this world.
A welter of voices can be heard when Nemo uses his Blue Water to open the gates to Atlantis — and boy, do they sound pissed at him. Why will be clearer after the revelations of Episode 22.
Similarly, the giant skeleton serving as the front entrance will make more sense after the Adam reveal in Episode 37 (the implication is that this was another early genetically-engineered human). The gateway responding to Nemo's Blue Water also hints the Blue Waters are master control keys to Atlantean technology (which is why Gargoyle is so desperate to acquire them, as he needs them to locate and access Red Noah).
Electra indicates the original Tower of Babel wasn't actually a weapon; that was just a secondary benefit of the technology. The meaning of her words will be revealed in Episode 35.
Atlantis did exist and was destroyed as per Plato's legends. So, then, where exactly did the Neo-Atlanteans come from? After all, for a new Atlantis to rise, there ''had' to be survivors. The missing link between the original Atlanteans and the Neo-Atlanteans will be revealed in Episode 22 and further explored in Episodes 31 and 35-36.
There are subtle hints even this early that Atlantis is what's left of Green Noah: The controlled environment, the semi-still-functioning machinery, the Nautilus docking with the Tower of Babel, and even the question of how such an advanced city could've been built this far underwater 12,000 years ago.
Surprisingly Realistic Outcome: The odds of Jean's Father having survived the loss of his ship weren't high to being with. Jean even acknowledged it back in the Pilot, but was hopeful he was wrong until Eiko confirms it.
Jean learning from Eiko the Sonar Officer that he served on his father...and that he was killed by the Neo-Atlanteans when their ship was destroyed.
The Chief Engineer's discussion with Electra during the funeral all but confirms Nadia is Nemo's daughter — or at least confirms they all know about the connection to (something that was implied by Electra's knowledge in Episodes 04 and 09-10).
Wrong Genre Savvy: Again, Jean (justifiably thanks to the late 19th Century setting) doesn't realize Science-Fiction has begun overtaking their Steampunk Action-Adventure (and that the Blue Water is not a jewel, but a highly-advanced piece of alien technology).
