Though the caverns do protect them, two of the colonistsnote perish before they are able to reach safety. When the survivors emerge after being rescued by the Enterprise, they find the lush, Earth-like planet of Melona IV has been turned into a barren wasteland.
The Federation's best expert on the Entity, Dr. Kila Marr, is brought aboard, eager for the chance to investigate an attack so soon after its occurrence. Her first question is how the survivors on Melona IV survived, when all previous encounters with the Entity resulted in total loss of life. Data theorizes that a unique combination of minerals in the cave rock was responsible for protecting them, but Marr seems unconvinced by this explanation. In fact, she doesn't like anything Data has to say. She specifically requests that he not participate on the grounds that he is related to Lore, who brought the Entity to the Omicron Theta colony, where the entire population, including her son Renny, was killed. However, Picard insists that Marr work with Data, the better to assess her objectivity.
On the planet, as they are conducting their analysis, Marr none-too-subtly suggests that the Entity may have spared the survivors because it had an accomplice among them, recalling Lore's previous collaboration with it. As Data is too Literal-Minded to pick up on her subtext, she outright accuses him of colluding with the Entity. Data takes her accusation in stride, reassuring the Doctor that he does not share his brother's misanthropic temperament, though it does little to placate her. Later, however, once one of Data's suggestions ends up revealing a method for tracking the Entity, her attitude starts to change.
The Enterprise beings its search. Dr. Marr shares her recommendations for how best to destroy the Entity, but is aghast when Picard insists on attempting to establish peaceful communications first. Riker also expresses reservations about this idea, especially after they hear word that it has claimed yet more victims aboard an alien ship. Picard overrules them, believing the Entity should be afforded the chance to live if it can be steered away from intelligent life in its search for food.
At his orders, Dr. Marr starts working with Data on a way of communicating via graviton pulses. Marr starts warming up to Data, even moreso when she learns how much knowledge he has of the colonists on Omicron Theta, her son included. She questions Data about Renny's life prior to his death, and even has him recite some of his journal writings with his Voice Changeling abilities.
When the Enterprise finally catches up with the Crystalline Entity, they begin sending it a series of graviton pulses designed to catch its attention. The Entity responds with a signal of its own, creating a pattern that implies intelligence. Then, without warning, Dr. Marr starts sending a much more powerful signal, destroying the Entity before anyone can stop her.
Giddy with revenge, Marr is placed under arrest. In her quarters, she pleads with "Renny" (actually Data) to absolve her of what she has done, and assure her that he understands why she did it. Data has no choice but to refuse, and tells her that, based on what he knows of her son, he would have been very sad to know what she did.
Tropes featured in this episode include:
- Alas, Poor Villain: Regardless of how villainous one considers the Crystalline Entity or Dr. Marr to be, both of their stories end tragically.
- Brutal Honesty: Data refusing his Replacement Goldfish status by the end.
- Death Glare: After watching his hopes for communication go up in smoke, Picard turns to Dr. Marr, and he is, of course, righteously pissed off.
- Downer Ending: The Crystalline Entity is destroyed by Marr before diplomacy has a chance to prevail. To rub salt in the wound, Data tells her in all earnestness that her late son would likely have been very upset by her actions, as her career is effectively ruined.
- Fantastic Racism: Subverted. Unlike some characters, who distrust Data because he is an android, it becomes clear that Marr distrusts him solely because of her hatred for his brother Lore and her grief over her son's death.
- Freudian Excuse: Marr has quite a large one with the death of her adolescent son at the hands of the Crystalline Entity.
- Heroic BSoD: Riker's Girl of the Week is killed by the Crystalline Entity while trying to save an old man. Riker takes it pretty hard, which initially leaves him more open to Marr's position.
- Hope Spot: It looks as though the Enterprise is succeeding in communicating with the Entity just before Marr destroys it.
- It Can Think: The episode builds on the idea that Lore was able to talk to the Entity by showing the crew trying to do the same.
- Moby Schtick: Dr. Marr's obsession with the Crystalline Entity. To drive the metaphor home, Picard compares the Entity directly to a sperm whale killing cuttlefish by the millions in Earth's oceans.Picard: It is not evil. It is feeding.
- Non-Malicious Monster: Although Picard acknowledges that they may have to destroy the Crystalline Entity if they can't communicate with it, he refuses to condemn it for destroying Federation colonies on the basis that it may merely be feeding, as any living being must to survive.
- "The Reason You Suck" Speech: Data basically delivers one at the end of the episode, as he tells Doctor Marr that Renny would not have wanted her to kill the Crystalline Entity in his name, and would actually be very sad at what his mother has done to her career to get her revenge.
- Replacement Goldfish: Towards the end, Marr starts to see her late son Renny in Data. She even calls him by her son's name once.
- Revenge Before Reason: Marr's grief over the death of her son—and her desire to avenge him—is the sole driving force behind her actions.
- Sanity Slippage: It becomes more and more apparent as the episode progresses that Dr. Marr's state of mind is not just unhealthy, but borderline unstable.
- She Didn't Make It: Riker regarding Carmen.
- Wide-Eyed Idealist: Picard sincerely believes it's possible to reach an understanding with the Entity. The Hope Spot suggests he may've been right.