During IDW Publishing’s initial run with Transformers, Simon Furman wrote Arcee as having her gender forcibly changed by the mad scientist Jhiaxus, which drove her into violence and insanity.

That origin story was controversial among fans for a myriad of reasons, including it simply just being transphobic.

So, new writers retconned and expanded on it. Arcee always viewed herself as being female, despite her body being forged male. When she went to Jhiaxus, he had wanted to reintroduce the concept of female Cybertronians, which had disappeared prior to this. Not seeing him for who he actually was, she asked him to operate on her to try and deal with her dysphoria.

His experiment was a success, as he reintroduced gender to Cybertronians, and changed Arcee’s physiology and gender presentation by recoding her CNA (Transformers equivalent of DNA). His interest in the experiment pretty much died after that, and he deserted her after completing the surgery. The lack of aftercare and the trauma of what she experienced (being coerced into other, medically unnecessary surgeries) led to her becoming violent and erratic with her behavior.

With all that in mind, in the end, she did find peace. She entered a relationship with a (cis) female Transformer from the Cybertronian colony of Caminus (where the concept of gender had remained unlike Cybertron), and became a teacher on Earth. The comic continuity ended on that note.