Summary:
The Federation is politically, socially, and economically shattered after the Borg attack [Destiny]. They want to get things back on track, so the Luna fleet is being sent back out to explore, to Riker's chagrin; he wants to help in the clean up efforts.
Tuvok and T'Pel's son and his wife were killed by the Borg. Tuvok is grieving and isn't sure he wishes to return to Titan, but T'Pel convinces him.
Titan's first mission back is to a water planet nicknamed Droplet; it's unique in that is mostly water, but appears to have lifesigns. They take a shuttle and land on a floating island that is itself alive, consisting of polyps like coral. Aili goes for a swim, follows a small fish into a section of water where there shouldn't be any life, comes across some larger fish, and is stung unconscious by a jellyfish before being rescued by the shuttle.
Later, Aili is swimming again with Melora Pazlar when she hears a distress signal from the "squales" (squid whales) that they've been observing. She and Pazlar are attacked again, this time by hundreds of tentacles (seemingly from a dead polyp), which drag Aili deep down into the ocean. The squales save her, carrying her to the surface, but are scared off when the shuttle comes to rescue her.
Tuvok has been late to his duty shifts for the last 5 months. Ranul covers for him and understands that his grief needs time to heal.
On Droplet, they see a creature they name "weather balloon", which seems to have an excess of sensory organs, similar to some of the smaller fish they've seen in the ocean. It is seemingly destroyed by a lightning strike, but when taken back to the ship, it revives when they play squale sounds, and starts making squale noises of its own. They conclude that the squales bred the creature to take readings and transmit them back. They decided that since they've been observed for over a week, it's too late to pull out for the Prime Directive and they need to make contact. Riker himself will go down to the planet, since the squales language is so musical, and he's a jazz man.
Aili dives down to communicate with the squales, but they stealthily pull her down deep with their tentacles. 4 hours last the rendezvous time, she resurfaces and tells Riker that she taught the squales some Selkie and opened a dialog with them.
One of the asteroids around the planet is on a collision course; Titan plans to use their tractor beam to redirect it, but find it's more dense than expected. they try to carve it up with phasers/torpedos, but the asteroids is filled with radioactive elements that cause a feedback on the ship, knocking the warp core offline.
Riker and Aili try to warn the squales of the impending asteroid, but they take it as a threat.
Titan fails to divert the asteroid, and actually changes its course to be closer to Riker and Aili's location. They try to outrun it, but they are hit by the shockwave and both are flung into the water. On Titan, Troi senses Will drowning. Dr. Ree says this is no place for a baby, grabs Troi, attacks Tuvok and nurse Ogawa when they try to stop him, and flees with Troi on his back, insisting that they have to get off the ship. Ogawa catches up to Ree as he's boarding a shuttle, and convinces him that he needs a nurse to help deliver the baby. Ree warps away before Titan can stop him. Tuvok tells Vale that Troi's fears about losing her baby were amplified by his grief over the loss of his son, which psychically influenced Dr. Ree, and he convinces Vale to let him take a shuttle to go after them.
The squales save Riker and Aili, healing them somehow and leaving them under protective custody on a polyp island.
One of the search shuttles is attacked by a large dreadnought creature with a hard shell and lots of tentacles. The shuttle gets away, but a squale us killed.
The squales tell Aili that the song of the planet has changed; the crew on Titan realize that the energy the asteroid absorbed from their phasers, tractor beam, etc. have caused changes in the planet's magnetic field--which is also why the squales recoil at their technology.
The squales move Aili and Riker onto a floating jelly-creature to get them out of the path of an incoming hurricane. Aili tries to spoon Riker to keep him warm and they get into a fight; she lets slip that their tryst years ago was improper for Starfleet officers who don't understand her culture, and he says shouldn't have slept with half of Titan's crew then.
Dr. Ree lands the shuttle on Lumbu, a pre-warp planet, and asks to be taken to a hospital, shocking the Lumbuans greatly and violating the Prime Directive outright. Troi is afraid that Ree has become so attached to the baby, that he might even keep it himself.
Cethente, a crystaline-like entity aboard Titan who can withstand ultra-high pressure, takes a bathysphere deep into the depths of the planet and finds that there are actually creatures living down there--but they have been poisoned by the asteroid's radioactive elements, and are acting hyper-aggressively.
Aili explains to the squales that she and Riker are dying because their biology is too different for this planet. The squales take her to a facility and explain that they can modify her biology to make her better able to survive on Droplet, but that it could make their memories hazy. After her fight with Riker, she's not sure she even wants to go back to Titan, so she considers this--though she's sure Riker won't want to undergo the process.
After analyzing Cethente's findings from the deep, they determine that the plankton which feed on the minerals deep in the ocean later rise up to the surface layer and are eaten by the creatures there. The poisoning from the asteroid may lead to a mass extinction event.
Tuvok and his team arrive at the hospital. He tells Troi that she is still projecting her anxiety and anger about the baby onto Ree because of the loss of her first child, and because Ree wanted to terminate this fetus before the Caeliar saved it. Tuvok admits that he feels shame for being angry at his son for dying to help others. Troi tells Ree how she truly feels, and her water breaks. The police storm the building.
Xin and Melora come up with a plan to use thousands of probes to generate a particle field in the depths of Droplet to neutralize the effects of the asteroid. Aili goes back to the islet to tell Riker about the squales' life-pods and finds him feverish and near death. She nurses him back to consciousness and apologizes; she says she was an irresponsible mother because she never listened to her own mother, who let Aili's sister be killed by a predator. She says they shouldn't undergo the metamorphosis and should hold out hope for Titan to find them instead.
Troi gives birth to her baby with little fuss. Ree immediately feels abashed for what he did when Troi's effect wears off; Tuvok places him under arrested, and Ree willingly goes along. The locals believe them to be spirits, so the Prime Directive violation may not be punished too severely.
Aili talks to the squales again and they say they'll help her find someone from Titan; they didn't know she couldn't contact them, since they take always being in contact with each other for granted. Elsewhere, Xin tries to tell the squales that Titan is going to fix their planet with probes, whether they like it or not, and they deployed armored marine beasts in response, attacking Xin's gig and the whole island. The squales tell Aili they have a probe they captured earlier, and let her use it to send a distress call, which Vale sends a team to intercept. Aili sings to the squales that Titan is trying to help them; after bearing her soul to them, they not only relent, but help deploy the probes.
It's not long before the squales notice the probes having a positive effect. Riker promotes Aili to lieutenant for saving the planet. Troi, et al return with the baby, safe and sound. Riker says Ree will still need to stand trial, but only as a formality, as he is grateful that Ree protected his child.
Titan's visit has convinced the squales to dust off their centuries-old space exploration program that they'd all but given up on. Riker thinks perhaps Starfleet can check back in on them in a few years. Riker, Troi, and Natasha Miana watch their first launch from the planet just 2 weeks later.