While Batiuk was a 23-year-old middle school art teacher in Elyria, Ohio, he began drawing cartoons while supervising study hall.

The more drama-oriented Funky Winkerbean featured story arcs revolving around such topics as terminal cancer, adoption, prisoners of war, drug abuse, post-traumatic stress, same-sex couples attending the senior prom, and interracial marriage.

Centered at Westview High School, influenced by Batiuk's alma mater of Midview High School near Grafton, Ohio,[3] the strip initially focused on several students: Funky Winkerbean, Crazy Harry Klinghorn, Barry Balderman, "Bull" Bushka, Cindy Summers, Junebug, Roland, Livinia, Leslie P. "Les" Moore, majorette Holly Budd (daughter of Melinda Budd, original majorette for Westview High), and Lisa Crawford.

From 1972 to 1992, the strip was highly gag-oriented, with humor coming from physical and prop comedy and surreal situations: running gags included the school's computer having become sentient and subjecting the students to its obsession with Star Trek; student "Crazy" Harry's ability to play pizzas like records; the school's winless football team; and band director Harry L. Dinkle's attempts to win each year's "Battle of the Bands," despite the contest always coinciding with a natural disaster (usually heavy rain).

Supporting characters included obsessive majorette Holly (who never removed her uniform), "Crazy" Harry (who lived in his locker), Jerome T. "Bull" Bushka[4] (the school's star athlete and Les's tormentor), and popular girl Cindy.

Rounding out the cast was the Westview High staff, including Principal Burch, counselor Fred Fairgood, secretary Betty Reynolds (who actually ran the school), football coach John "Jack" Stropp and Dinkle.

It was established that Funky, Les, Cindy and all the rest of the previous cast had graduated from Westview in 1988; their college years were skipped, and the story continued in their adulthood.

Though humorous storylines remained a mainstay, the strip also examined subjects more traditionally associated with soap opera or serialized comics.

He was saved when his Afghan companion Kahn managed to knock the mine away, only to be punched out for selling the Stinger that killed his fellow troops.

Following another round of chemotherapy, her cancer appeared to go into remission again in early 2007, but on May 9, 2007, her doctor revealed that her medical charts had gotten mixed up and her disease was not only progressing, but had become inoperable.

The series polarized the comics community, with Batiuk being both praised for dealing with the topic and criticized for his graphic depiction of Lisa's slow deterioration and ultimate death.

Readers got a preview of the new-look feature starting with the October 5 strip in which a middle-aged widower Les talks to an unseen psychologist about events that immediately followed Lisa's passing, which are then depicted in flashback form.

The October 21 strip[14] shows a younger Les talking with Summer about death in general to help her understand that of Lisa's, before switching to the new-look Moores in the closing frames, and the first week of strips that followed, following the Moores participating in a Making Strides walk, have a banner saying "Act III: Ten Years Later" in the first frame (an "Act III" statement directing readers to the official website was discreetly included in fine print for some time afterward).

He also promised that despite Lisa's death, she will remain a presence in strip through flashbacks, remembrances, and a series of videos she recorded for daughter Summer just before she died.

[16] While a few of the mainstay elements—most notably, storylines revolving around the Westview High School band and now-retired director Harry Dinkle, and classroom spot gags—reappear in Act III on occasion, the focus once again is on dramatic storylines with continuing story arcs: Wally Winkerbean—who had returned to Iraq before the relaunch—is not in the core cast as shown on the Funky Winkerbean Web site, and it was also revealed that Becky had remarried (John Howard, owner of the Comics Emporium) sometime in the 10 years after Lisa's death.

Batiuk also revealed that a "clue" to Wally's fate could be found in the October 11 strip, which features Les getting mugged in New York after Lisa's death after walking past a newspaper vending machine with a headline saying "Soldiers Taken Hostage.

"[17] Several strips made allusions to Wally's disappearance, including one featuring Becky Howard's car having a POW/MIA bumper sticker and her placing a U.S. flag on an unidentified grave.

Although the recovery aspect of the accident storyline continued into the fall, the flashback scenes ended when Funky regained consciousness at the hospital.

When a group of students led by Summer Moore supporting LBGT couples attending the prom plan a counter-protest, principal Nate Green defuses the situation by calling a school assembly and announces that gay couples will be allowed to attend the prom, and that he will not have intolerance at Westview High School be a policy issue during his tenure.

[19] Some time after Lisa's death, Les begins dating Cayla Williams, a black teacher at Westview High.

In January 2013, Fred Fairgood—now retired as principal of Westview High—suffered a major stroke and was barely alive at the hospital; he is later shown to be recovering at home, although he is disabled.

In 2011, before Fred Fairgood fell ill, another longtime Westview staff member—Jock Strapp, the former football coach and physical education teacher—had died of prostate cancer, although this was acknowledged only briefly.

"[24] The Comics Curmudgeon also makes frequent reference to the seemingly unremitting gloom of the strip, calling it "a black hole of bleakness and depression and cancer from which no joy or laughter can escape.

[29] In a September 2009 storyline that many readers[30][31][32] also interpreted as Batiuk's addressing of the strip's latter-day bleakness, a group of parents protested a school production of Wit because the themes of cancer and death offended them.

[37] A year earlier, as part of a long series featuring multiple storylines, Pastis remarked to Pig that serial strips handle long stories better and featured Funky, Holly, Lisa, and Les in a parody referencing, among other things, Lisa's breast cancer.

[38] Two minor characters have been spun off into their own strips: the bus driver Crankshaft in 1987 and the talk show host John Darling in 1979.

In Funky Winkerbean, Les Moore wrote a book about Darling's murder and solved the case in a 1997 storyline.

Batiuk also occasionally parodies covers of classic Silver Age comics to comment on storyline elements in the strip itself.