At the start of the movie we learn that Duvall's character - a marine fighter pilot - is not only a strict disciplinarian, but he's also a jokester who loves to pull all kinds of practical jokes on his comrades, such as pretending a can of soup is vomit. His nickname is "Great Santini" but it's never really explained. In this classic scene, he thinks his buddy is in the stall next to him, and his prank goes wrong ---
He also has a bit of a drinking problem. But as his superior officer tells him, he's a great leader, and gives him a new assignment training pilots in South Carolina where he moves with his wife and 4 children (the film is set in the 1960s) Here's another scene with Duvall with his new squadron:
I also love the part where he meets his new maid, played by Theresa Merrit of the 70s TV show That's My Mama!. She steals the scene when she declares she can take a punch just like a man and challenges Duvall to a fight. It's hilarious. There are some other funny bits in the film, such as when his daughter gives him a taste of his own medicine when she jokes that she's been impregnated by a pacifist.
But the movie is not solely a comedy, though there are quite a few light moments. There are also some serious and touching moments, especially near the end.
The main focus of the story is on Duvall and his oldest son played by Michael O'Keefe. This is the only other movie I've seen with O'Keefe besides Caddyshack; I was really impressed with him in this role and all the scenes he has with Duvall - the arguments, fights, and even moments of bonding, especially when Duvall takes him out for a drink on his 18th birthday and he has a funny "drunk" scene. I also love the scene where Duvall wakes the son up at 4 in the morning to give him his birthday gift - his old WWII bomber jacket.
But throughout the film there is tension between the two. Duvall puts pressure on him to be the best, whether its being the best future pilot or being the best athlete on the team.
There's a subplot in the film is about O'Keefe's black friend (Stan Shaw) who stutters and is teased by some of the local white racists. At first I wondered if this subplot was necessary. but as I thought about it more I realized that it is meant to show real hate and its consequences. At the end of the film we realize that Duvall and O'Keefe never really hated each other, even if it feels like hate.
With Blythe Danner (as Duvall's wife).