In The Squid and the Whale (2005) written and directed by Noah Baumbach, Jesse plays the fictionalized version of the real adolescent Baumbach as Walt Berkman, the petulant son of a washed out littérateur, Bernard, in the process of divorce from a promising novelist, Joan (played impressively by Jeff Daniels and Laura Linney). Walt whines at his mother "you disgust me" and feels proud of his elitist egomaniac father (who demeans ordinary people as "philistines") in the first part of the film, but he'll progressively communicate more with his mother looking for comfort; in this time lag he's oblivious to his nice girlfriend Sophie (Halley Feiffer) while he maintains a childish obsession with a sexy student, Lili (Anna Paquin). Walt powerlessly observes his father's appalling despondency and he fantasizes about being intimate with Lili, who (having once plagiarized one of Lou Reed's verses) knows of Walt's secret rip-off of a Pink Floyd song that he's been passing as his own. In a double climactic father/son denouement, Bernard makes an elegant farewell citing Belmondo's 'Déguelasse' line to Jean Seberg in Godard's film À bout de souffle, and Walt accepts the scary uncertainty caused by his limitations: "The scary fish at the Natural History museum. I was always afraid of the squid and the whale fighting. I could only look at it with my hands in front of my face."
It's a fine dramatic (and marine) note to end this autobiographical film, since our visual system (primate) is made to appreciate yellow and red colors but below sea level there is no red light so male fish, when trying to attract females, only see blue tones.
In The Education of Charlie Banks (2007) directed by musician Fred Durst, Eisenberg plays Charlie, a bourgeois young man whose acquaintances belong to an uppity college environment during the '70s at Brown University in Rhode Island. He's running away from a bad boy Mick (Jason Ritter) while he tries unsuccessfully to invite the "very much out of his league" Mary to a lunch. Among decadent parties, references to The Great Gatsby and Derrida, Charlie (a "cold bitch") flips a "fuck off" to Mary when he's the object of her condescending derision, learning a difficult moral lesson when he confronts Mick in the end.
Eisenberg appeared in indie films such as The Living Wake, and One Day Like Rain in 2007, and then was cast in a supporting role in The Hunting Party, playing Benjamin Strauss, the son of a TV network executive who's desirous of being taken seriously in journalism field, joining an unsteady twosome of veteran reporters embarking on a hunting mission to capture The Fox, the number one war criminal in Bosnia.