- Dracula threatening Dr. McNinja through Gordito does not work. Why? Because the doctor believes that strongly in Gordito's abilities and he's right.
- The zombies from Revenge of the Hundred Dead Ninja have enough humanity left to remember what was most important to them. We see one such zombie make it to his daughter's school play, tearing up joyfully. Whilst eating the guy next to him.
- SEAN MCNINJA DOES NOT LIKE BEING HUGGED PEOPLE.
- "You didn't pack enough." May double as a Tear Jerker.
- Mitzi's expression and the subsequent hug make it doubly so on the next page.
- Yoshi telling Dr. McNinja that he's happy that the doctor is alive. Heck, McNinja saying he's happy that Yoshi's alive counts as well! Considering that these two have had a rocky relationship in the past, only ever working together when Gordito is in trouble, that the both of them are glad to see each other alive and well is definitely a nice touch.
- During the montage of various scenes after the humans won the war against the dinosaurs, we finally get to see Gordito and Yoshi reunited. The look on that raptor's face? Yeah, he missed his human.
- When Ron, Steven, and the citizens of the Radical Lands arrive in the world, King Radical is just so overjoyed to see them. As terrible as how they arrived is, KR is seeing his friends and people for the first time in possibly years after mulling around in a considerably blander world. Also since the Radical Lands are dying, them appearing means that he's saving lives.
- How does Dr. McNinja celebrate defeating King Radical's plan? By calling up a pizza place to get the Friend Brothers back in business as a way to make amends.
- The good Doc Mercy Killing his own mentor Ben Franklin, stuck on the Mortal Plane as a headless horseman by finally dealing with his Unfinished Business. Just buying a pizza he promised to take him out to celebrate for.
- The last page of "Why a Gorilla?" has two: Dr. McNinja defending Judy against a rude patient and when she thanks him, he responds in sign language.
- The whole story finally shows Doc and Judy communicating with each other, showing us why Judy puts up with the crap working with Doc puts her through, and that the two really are friends.
- Dr. McNinja is largely unaffected by the Negazone, an amalgamation of all the worst fears to every intruder trapped within. Unaffected, that is, until Negazone!Gordito shows up and tells the doctor that he is a bad role model.
- After some brief resistance and denial, Dr. McNinja finally concedes... by saying he'll have a talk with Gordito when it's over and see what he needs.
- Doc's meeting his Grandfather for the first time as a kid has some sweet moments considering half the story he's trying to teach Doc to justify murder.John: Hanging out with grandpa... that means ice cream for breakfast?Doc: Yes it does.
- The Doctor's Final Thoughts on The End: Part 1 concludes with him finally seeing a patient who's appointment had been pushed back numerous times, despite standing in the burnt remains of his office.
- The ghost wizards' reunion. The ghost wizard that fought Dr. McNinja in his youth was being sincere after all.
- Mitzi McNinja, the one person in Dr. McNinja's life who was always critical of his decision to become a doctor, is finally proud of her son.
- Another heartwarming moment: the universe has turned its back on McNinja, according to the ghost wizard, so are we about to see him bust into the villains' lair for one final showdown, completely outnumbered, all alone? No. Not in the slightest. Or at least, not at first. It gets completely reversed when his own family and friends betray him, with him not knowing why.
- It turns out it was to save Gordito, and even then it's shown that they had to tie up Martin because he didn't want to betray the Doctor. And judging by their faces, his parents aren't exactly happy about betraying him.
- Doc finally gets through to his poor confused cloned self and convinces him that he's just a little out of his head, not dying of Clone Degeneration.
- The look on Dan McNinja's face when Doc kills King Radical once and for all. Despite everything that's happened, despite all his gruffness and disapproval of Doc's choices, that is the look of a father bursting at the seams with pride for his son.
- And shortly afterward (although it comes at a tense moment) Mitzi not denying that Gordito is like a son to her.
- The final page of the comic◊: the Doctor continues to practice medicine, under the name Pat Goodrich, after his late friend.
- As far as spirit of vengeance goes, the Nasaghast are really kind to the astronaut and no place or timeline is too far to stop them from protecting their living co-worker.Nasaghast: Knew you would survive... You remain...NASA astronaut... Punish all that would harm you.
Heartwarming / The Adventures of Dr. McNinja