Alyssa is tangentially connected to characters in Smith's other films (as, indeed, are most of the major characters in the "View Askewniverse" films): She is the older of the Jones sisters, which include Trish "The Dish" (featured in Mallrats) and Heather (featured in Clerks.) She had a brief fling with Shannon Hamilton (featured, along with Trish, in Mallrats), and is the former best friend of Caitlin Bree (featured in Clerks.)
In Chasing Amy
She is introduced in Chasing Amy as a self-identified lesbian comic book artist whose feminist comic, Idiosyncratic Routine, barely figures in the "Big Pecs, Big Tits, Big Guns" world of graphic novels. She meets Holden McNeil, the co-creator of the far more popular Bluntman and Chronic, at a comic book convention and they hit it off, persuading Holden to believe she is attracted to him. At a party a few nights later, however, he discovers where her romantic leanings truly lie when she publicly makes out with her lover, Kim. Embarrassed, he withdraws from her completely.
The next day, Alyssa shows up at Holden's door, offering friendship, and they form a bond after she explains the mechanics of lesbian sex, information he receives with his jaw dropped to the ground. The two become close friends, much to the annoyance of Holden's best friend and Bluntman collaborator, Banky Edwards, who is homophobic. It is also implied that Banky is jealous of Alyssa's closeness to a friend that "he had first."
Holden, however, is still in love with Alyssa, and breaks down and tells her so one night. At first, Alyssa is angry that he would ask her to completely change her life for him, but eventually gives in to romantic feelings she herself had harbored for him and becomes his lover. She reasons to herself that there was no point in closing herself off from a viable relationship simply because Holden was not of the gender she usually preferred. Her lesbian friends ostracize her for her "treason", but she is otherwise quite happy; in a very short time, she has fallen in love.
Weeks later, Banky confronts Holden with secrets from Alyssa's past — namely, that she had indulged in a ménage à trois in high school (earning the nickname "finger-cuffs") with two men. This shatters Holden's idyllic notion that he was the first man she had been with, and he angrily confronts her during an ice hockey game. She refuses to apologize for her past sex life, which makes him even angrier.
After advice from recurring Smith characters Jay and Silent Bob, however, he realizes that he is in danger of losing her forever. He calls both Alyssa and Banky over to his apartment to talk, where he confesses that her past sexual exploits make him feel small and inexperienced in comparison. Holden also tells Banky point-blank that the hostility between him and Alyssa comes from subconscious sexual desire for his best friend. Holden's solution is that the three of them should all have sex together. Banky eventually (and reluctantly) agrees, but Alyssa refuses, saying she has already explored such territory and didn't find what she was looking for, and that she is hurt that Holden would want to "share" her. She breaks up with him right there, and leaves, stating that although she loves him, she will not be his whore. A relieved Banky, happy that he will not have to go through a three-way, also leaves, and Holden is alone.
A year later, Alyssa is once again exclusively dating women, and Idiosyncratic Routine is topping the charts (Bluntman & Chronic, meanwhile, has ended its run, after Holden sold the rights to Banky). Holden shows up at one of her book-signings, and the two have a quietly emotional conversation in which they wish each other well. Holden gives her a comic he drew called Chasing Amy, which details their relationship, as a way of letting her know how he feels. It is left ambiguous whether they ever see each other again.
Alyssa makes a cameo appearance in Jay and Silent Bob Strike Back, in which she and Trish exit a showing of the movie version of Bluntman & Chronic, which neither of them like (even though Alyssa admits that it was "better than Mallrats.") When Trish asks Alyssa why she doesn't make a movie out of Holden's Chasing Amy comic, Alyssa lights up a cigarette and replies, "That would never work as a movie."
Chronologically, she is first seen attending Julie Dwyer's funeral in the animated short Clerks: The Lost Scene, in which she has a brief conversation with Dante Hicks, telling him how Julie Dwyer died and why, but not before swearing her hatred of Randal Graves. Once Randal spots her, he says "Hey! Fingercuffs!" She tells him to go to hell and storms off.