- How about the fact that the FBI suspect Indy - a decorated war hero - of espionage after being forced into aiding and abetting a KGB operation on American soil? The audience knows that Indy did it against his will, but even then the two agents don't (despite General Ross saying otherwise) and are fully willing to intrude in Indy's private life for more evidence.
- Indy looking at a photo of the late Henry, Sr., complete with the musical cue from the previous film.
- Made even more bitter since Sir Sean Connery passed away in his sleep on October 31st, 2020.
- Early on in the movie, Indy tells Stanforth that Marcus and his father both died, and with Mac betraying him, he's completely alone. This brought tears, only for a reprise of crying when Indy finds Marion and Mutt again.
- Not to mention the way John Williams' score is precisely aimed to work these moments to the hilt. It is now hard to hear the Grail theme without tearing up at the thought of Henry Jones Sr's death.
- When Mutt and Indy go to the asylum where Oxley was held after going mad. He's trying desperately not to cry at the evidence that the man he saw as his father went insane.
- Mutt's angry reaction when he finds out Indy is his father. Thankfully he warms up to the idea after a while.
- Mac's sacrifice. He wasn't that great a guy, but he was still Indy's friend, and Indy wasn't going to let him go without a fight. The film is a bit ambiguous if Mac deliberately sacrificed himself so Indy and the group would have time to escape, or if he just couldn't hold on any longer, but either way, it's a surprisingly tragic death for an unrepentant villain.
- Irina Spalko's fate is slightly sad in that despite what she kept saying about using the power of the skull to help the USSR rule the world, her true heart's desire was nothing more than wanting answers to the questions man has asked since our humble beginnings. Unlike Belloq's greed, Mola Ram's delusions and Donovan's obsession with obtaining eternal youth, Spalko's desire seems almost innocent by comparison.
- Innocent, perhaps, but not very bright. Maybe the expression "there are some things man was not meant to know" is the best way to put it.
- Especially given that the novelization reveals that the aliens even forcefed her knowledge of ancient eldritch beings. Also, she very much felt her dematerialization.
Tear Jerker / Indiana Jones and the Kingdom of the Crystal Skull