S01 E02 Dead Reckoning
- Command Master Chief Jeter leads the enlisted crew in a candlelight vigil (with chem lights in lieu of proper candles) for their loved ones, almost none of whom can be located.
S01 E08 Two Sailors Walk Into A Bar
- Crosetti is killed just as he's helped pull off a successful mission and lost his status as The Load.
S01 E09 Trials
- When Maya dies, her crewmate, Miller, says she will be missed.
- When it looks like the vaccine isn't working, Quincy prepares a morphine injection to send the volunteers to a painless death. Luckily, Dr. Scott has her "Eureka!" Moment right then. It's still a pretty heavy moment.
S01 E10 No Place Like Home
- Chandler finally finds his family and is able to give them the cure but also finds out that he was too late to save his wife.
S02 E01 Unreal City
- Quincy's Dying Moment of Awesome.
- Dr. Scott goes out into Baltimore to provide the cure to the sick. But she eventually runs out and only has enough for one more dose as a mother and child wait for their turn. The mother tells Dr. Scott to give it to her son so that he, at least, could have a chance.
S02 E02 Fight the Ship
- Lt. Granderson is so distraught by her mother's actions that she has to be forcibly dragged back onto Nathan James because she'd rather die than face her shipmates.
- The crew of Nathan James having to say goodbye to those who died while retaking the ship.
S02 E03 It's Not a Rumor
- Some crew were able to find their families but others aren't so lucky.
- Chief Engineer Garnett breaks down in tears after discovering her husband's and daughter's names among the papers documenting the deceased at a local hospital.
- Commander Slattery finds the camp where his wife and daughters were staying but only finds their belongings. Although Tex encourages him to stay behind and look for them, Slattery forces himself to return to the ship, tearfully leaving a note and three doses of the cure for his family at their home should they return.
S02 E08 Safe Zone
- President Michener reveals that he had brought his son to Florida in violation of CDC quarantine protocols, and this was highly likely as the reason for mass deaths in Florida, including his own family. Even worse, his wife had asked him to euthanize his daughters when they got sick.
S02 E09 Uneasy Lies the Head
- Towards the start of the episode, Michener is still so unready to take command that he suffers a panic attack while trying to decide what to have for lunch.
- Ravit's disillusionment with the world and her belief that Humans Are Bastards:I was stationed in the West Bank for three years, another two in Gaza. Thought I'd seen everything, then this pandemic broke out and I thought, maybe now we have this common enemy. We even have this cure that we want to give to people. Maybe, just maybe, we'll stop killing each other. But nothing's changed. It's all the same.
S02 E13 A More Perfect Union
- The crew are sitting at a bar and sharing stories of a comrade who met his end earlier in the season. They begin one-by-one toasting the various crewmembers they've lost since the mission began.
S03 E07 In The Dark
- In the opening, Garnet, Ray, Miller, and Jeter sit down for their first meal since being rescued, but none of them are hungry, but they're also painfully aware that the staff made this meal just for them. After a long awkward silence, Miller breaks down crying.
- After seven episodes of being badgered by a particularly scummy journalist who is openly trying to destroy him on behalf of one of the regional directors, and fearing that Chandler and his crew have been lost, which would strip him of one of his most vital allies at a time where he needs every ally he can get, Michener finally reaches his breaking point and (seemingly) commits suicide. And then just to put the boot in for good, Michener's top aides essentially throw his programs under the bus for short-term political gain in the aftermath.
S03 E09 Eutopia
- After a gut wrenching Macross Missile Massacre by Chinese land batteries, the destroyer Shackleton is sunk with all hands. Needless to say, the anguish among the Nathan James bridge crew is palpable at hearing her destruction.
- It's revealed that Michener was in fact murdered.
S03 E11 Legacy
- The regional leaders, plus Shaw, clearly intend to relegate Presidents Michener and Oliver to footnotes in the history of the United States, rather than being memorialized as heroes for helping to re-establish the country on a firm footing.
- Japan has not only lost millions to the first wave of the plague, but since then has lost many more thanks to Peng's use of biological warfare, with many priceless and irreplaceable cultural/historical artifacts destroyed as a final dick move by Peng. While some have survived in Japan (a small percentage are naturally immune, the plague is only about 90% fatal, and some have likely managed to avoid both the plague and Peng's anti-cure), their population is likely around a million or so at best (from 127 million pre-plague). If they can recover, it will be a long, slow, difficult process.
- Takahaya's determined stoicism after the fight to retake the Japanese National Archives. The blood transfusions are no longer working for him and his wife, and Peng's bioweapon prevents the cure from working on them. When Chandler offers to take him home, he looks around and declares, "I am home." Knowing he'll die either way, he wants to spend his last days on his native soil, doing what little he can to preserve what's left of Japan. After his Heel–Face Turn, it's heartbreaking.
S03 E12 Resistance
- Kara, Oliver, and Tex arrive in Las Vegas, only to find it's nearly abandoned after the supply lines got cut off. The only people around are scavengers and an old man who's too crippled to leave and is slowly starving to death. Shaw and her minions have a hell of a lot to answer for.
- Kara thinks she's lost Danny as well as all her friends and comrades on the Nathan James. Her Heroic BSoD is hard to watch.
S03 E13 Don't Look Back
- Tex's death. If that wasn't heartwrenching enough (and for obvious reasons, it hurt), it also served as the final straw that broke Chandler and made him resign from the Navy.
S05 E05 Warriors
- This episode shows some cracks starting to form in some of the series' major relationships:
- Towards the beginning of the episode, Kara and Danny are reunited, but Kara is still grieving the death of her best friend, while Danny can barely muster the effort to comfort her because he's still recovering from months of being on the front line. It's also revealed that he's been avoiding Frankie since his return, and one of his attempts to hang out with his son shows why; when Frankie accidentally pulls Danny's combat knife out of its holster, Danny yells at him, scaring the poor kid so badly that Kara has to calm him down.
- Chandler's attempt to reconnect with his kids after having left them on their own to go back to the Nathan James, is an utter disaster. Ashley has grown tired of him never being around, and when he tries to reassert his fatherly control, it leads to a screaming match between them that ends with Ashley delivering an Armor-Piercing Response that stops Chandler dead in his tracks.
- While the fundraiser is mostly full of humor and heartwarming moments, it delivers a poignant tearjerker when Miller comes across a book recounting the history of the Nathan James, and finds the chapter about the cure trials, and reaches the biography of Maya Gibson, one of the trial subjects who died. His expression suggests that he's just had some old wounds re-opened.
S05 E09 Courage
- Burk's death. He managed to survive to the penultimate episode and rise through the ranks, only to take a spear through the chest during what should have been a routine mission. The worst part is, when Green finds him, it looks like he might have gotten lucky and the body armor stopped the spear, but then Green turns him over and you see the spear coming out his back...
S05 E10 Commitment
- The sinking of the Nathan James. After five seasons of pulling through situations that should have destroyed it several times over, it gets absolutely pounded by the mystery ship, and Kara is forced to give the order to abandon ship.
