Are female transformers ever shown in any origin stories where the autobots are fighting the war on Cybertron? I know some show up in Transformers:Beast Wars but are any seen on Cybertron during the war with the Decepticons? Are there any hints at why they were built since most robots in disguise are 'male'? Thanks in advance.
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Oh certainly! Female Transformers (or femmes, or fembots) have been around since the 1980's show, and have always been canon to their respective continuities.
In fact, 4 female Transformers have appeared in the film series already:
Arcee
Chromia
Elita-1
Alice
In War for Cybertron (video game), we are shown Arcee, and Slipstream who are both female robots who fought in the war.
The G1 cartoon shows several females in flashbacks on Cybertron, including Arial (who became Elita-1) and Chromia.
As for origin, the more recent versions of Transformers (like "Prime") have done away with the idea that Transformers were "built" like machines, and gone with the idea that they're just an alien race, and they happen to be robots. The original 13 however, were built by Primus, and one of them was a female named Solace, so she was probably the ancestor of the newer females.