I’m gonna answer this in the form of what-ifs and personal theories and also based only on the Prime 3 pirates so here goes:

Since their real body is a limbless leech, I don’t think they could have utilized tools on their own. They were probably the weird alien fish equivalent of dolphins. UNTIL

Maybe a certain species of alien bird with no sense of boundaries was watching these little worm guys and seeing their potential. So they decided to show up and be like “hey u guys want limbs and also space travel?”

There’s definitely a pattern in the series of the Chozo being responsible for horrible disasters that kill a bunch of people. Like Metroids, you know because SOMEONE thought virtually-unkillable killing machines were just the dandiest solution to get rid of another unkillable killing machine. And also uplifting the Bryyonians and we all know how that went. So I think it would be perfectly in-character for them to also be responsible for the Space Pirates being a threat, (and also destroying their own Homeworld hey just like Bryyo) when they would have otherwise been harmless alien fish on a perfectly healthy planet.

I mean think about it, they spend their whole lives in the ocean with no arms and then suddenly someone shows up, sticks them on land, gives them hands and is like alright have fun with that sensory overload mate. And then they go crazy developing and dominating every inch of their planet’s surface for no other reason than NOW WE CAN. And then that one planet just isn’t enough, so they use their newfound legginess to make laughable attempts to conquer every other planet too! 

And the rest is history.

moira overwatch april 4th