* The bit where it seems that Indy has gone over the cliff in the tank, and his father and friends are staring over the side of the cliff, stricken. And then Indy appears beside them, battered but alive, looking over the cliff in confusion to see what they're all looking at. And then -- the truly tear-jerking bit -- Indy's father embraces him in a bear hug for the first time ever and chokes out "I thought I'd lost you, boy!"
** Henry immediately filled with regret after thinking his son has died:
--> Oh, God. I've lost him, Marcus. And I never told him anything. I just wasn't ready, Marcus. Five minutes would have been enough.
** It's made even sadder in the Junior Novel and Adult Novelization, where Henry realizes that he was so obsessed with the Grail, he was never a good father at all and never even told his son that he loved him.
* When Henry's shot by the Nazis and Indy falls to his knees, frantically trying to stem the bleeding, his hands trembling ... it's devastating to see that sarcastic bastard so shaken.
** After all the bickering they engaged in, both dramatic and comical, seeing ''Indiana Jones'' actually shedding tears when his father was shot is proof that he ''did'' still love and respect him.
* Elsa's death due to her inability to let the Grail go, and Indy's near-death for the same reason until his father intervenes.
** "Indiana... Indiana... ''let it go''."
* The scene at the crossroads, where the argument between the Jones' about which direction to go gradually takes on more personal tones as old wounds are brought up for what, it's implied, is the first time.
-->'''Henry Jones:''' The quest for the grail is not archeology, it's a race against evil. If it is captured by the Nazis the armies of darkness will march all over the face of the earth. Do you understand me?\\
'''Indiana Jones:''' This is an obsession, Dad! I've never understood it. Never! ''[Bitterly]'' Neither did Mom.\\
'''Henry Jones:''' ''[Deeply hurt]'' Oh yes she did. Only too well. Unfortunately, that's why she kept her illness from me. Until all I could do was mourn her.
* A short one, when he finally gets the diary from Elsa. The argument itself is pretty sad.
--> '''Elsa:''' You came back for the book? Why?
--> '''Indy:''' My father didn't want it incinerated.
--> '''Elsa:''' Is that what you think? I believe in the Grail, not the swastika.
--> '''Indy:''' And yet you stood up to be counted with the enemy of everything the Grail stands for. Who gives a DAMN what you think?!
--> '''Elsa:''' You do!