* "Miss Murray, though I am a beast, do not think that I am stupid. I know that I am hideous and hateful. I am not loved, nor ever hope to be. Nor am I fool enough to think that what I feel for you is love. But in this world, alone, I do not hate you... and alone in this world, you do not hate me. I... I would be grateful if you left me now. Go quickly, woman. Go before I break your jaw."
* "Oh, it's thundering so fast... so very fast. I was right, then, about this world. Always I knew that Heaven would be the cruelest of places. Farewell, my perfect Mina."
* Regardless of what you may think [[FanDisservice concerning how pleasant it has been to look at so far]], the moment where Allan explains his reactions to seeing Mina's scars for the first time and his request to see them again is quite touching.
-->'''Allan:''' I want to see your scars. I want you to know that they are not a difficulty between us. I have my faults, Mina, but I'm a better man than that... they're part of you. Part of your body, your past, who you are... Mina, there's no part of you that is not beautiful.
* In Vol. 2, the brief moment where the young James Grey shows amazement at the ''Nautilus'' and declares he'll build his own someday, earning Nemo's encouragement. Just like in his original book, no matter how bad things get, Nemo can still appreciate wonder over science.
** While the 1950's League the adult Grey worked for might not have worked out, his invention certainly did, and ''Professor'' James Grey did indeed fulfill his dream.
* In Volume 3, Jenny Nemo refusing to use the Fire of Life like Alan and Mina had done, prefering to await the natural end of her life, hoping to be reunited with her husband, Broadarrow Jack, in the afterlife, knowing that her daughter and grandson will keep her legacy alive.
* YMMV on this, but one of the references in the Travellers Almanack mentions that a colony of Deep Ones, the fishmen from ''TheShadowOverInnsmouth'', were taught to sing and dance by the captain from ''HMSPinafore'', and have adapted human musical culture as part of their own.
* Quatermain to Sawyer, [[spoiler: [[TearJerker moments before he dies]].]]
--> '''Allan Quatermain''': May this new century be yours, son, as the old one was mine.
* The Jekyll and Hyde personalities making peace to save the ship.