Penny Arcade, the gaming webcomic which has expanded into a multinational brand covering everything from journalism to conventions, yesterday plunged itself back into controversy by re-opening a wound from long ago.

In 2010, the "Sixth Slave" comic ran on the site, with a pretty blunt gag about being "raped to sleep by the dickwolves". That sparked a small amount of protest, if nothing else showing that 2010 was, in some ways, a surprisingly different time to 2013. Penny Arcade's response was another comic, a blog post and comments making many of the same arguments that still occur in disputes over rape jokes today: that rape jokes are no different from bestiality jokes, that no-one rapes because of a joke, and that it's just comedy anyway.

As is the nature of massively-distributed online arguments, the whole thing spiralled out of any one person's control. It's now far too big to summarise, but if you're interested in what went down from then on, a comprehensive – if obviously subjective – timeline has been compiled.

But perhaps the most questionable response of Penny Arcade themselves was to start selling "Team Dickwolves" t-shirts. Even taking the pair's defence, that there's no problem because the comic features "an imaginary person… raped imaginarily by a mythological creature whose every limb was an erect phallus", at face value, selling merchandise putting that creature front and centre was a needlessly provocative move.

A month and a half later (this now six months after the original strip), the merchandise was pulled from the store. That wasn't the end of the matter, not by a long shot. In fact, search traffic for "dickwolves" peaked a month later as Mike Krahulik and Jerry Holkins, the artist and writer of the comic respectively, continued to defend their initial reaction. The discussion bubbled on for months, but as a mark of contrition it was important. The issue eventually faded away rather than coming to any natural ending, until yesterday, when it returned with a vengeance.

Yesterday, during the closing stages of PAX, Penny Arcade's convention in Seattle, Krahulik told a panel that he thought "that pulling the dickwolves merchandise was a mistake," to cheers from the audience. Robert Khoo, the company's President of Business Development, who was acting as chair for the discussion and had been behind the decision to stop selling in the first place, agreed, saying that doing so was "a way of engaging", which they now try not to do "in these type of things".

For many gamers, the dickwolves debate three years ago was the first time they had been introduced to a number of concepts, from the ideas of triggering material and rape culture. Some reacted defensively, as people being exposed to these ideas still do today; but others examined the opposition and saw where it was coming from.

Today, that excuse is not available. These ideas have been mainstreamed to the extent that Krahulik and Holkins cannot get away with pretending that it's only a vocal minority who see problems with using rape as a punchline which don't extend to problems with using murder in the same way. But the last three years have not seen the pair toning down the rhetoric. From Holkins writing about the "censorship" of criticising a game's exaggerated female characters to Krahulik being dismissive of trans people (leading to a $20,000 donation to the Trevor project), there have been no end of sub-dickwolves controversies, causing one prominent indie developer to pull out of their shows entirely. The Financial Post's Daniel Kaszor summed them up in an article titled "Penny Arcade needs to fix its Krahulik problem".

But by reopening the wound that first suggested that all was not well at Penny Arcade, Krahulik has also firmly reopened the debate about whether the pair can be trusted with the power they have in gaming. The contagion of the rest of their properties starts at the top, and it's looking less and less likely that they can avoid getting part of the taint. The PA report is a good news organisation; PAX conventions seem like genuinely good fun; and Child's Play raised over $5m to buy games for children's hospitals last year. All three started with a boost from the PA brand, but will it become a millstone dragging them down instead?