Alright, we all know that Hera is capable of just about anything. We just need some crazy ideas to start off with. Here are a couple:
Spatial construction platforms : Cargo ships drop these as their special weapon. They can construct moors, artillery drones, relay stations, power stations, or a special racially based construct (Human outpost, Obish shipyard etc). After building, they self destruct. The platforms are technically "planetoids," so they get around the "no moving builders" restriction.
Warp inverters : Eleejeetian dreadnoughts drop these special "mines." Within a certain range, about 256 pixels, they will target any warp in/out flare and detonate it for an instant kill of any ship it hits. The idea is to get ships to stay and fight or slowly limp away if they wish to retreat. A rather unorthodox use of this would be to take a cruiser into hyper outside range and fly out of hyper on top of, say, a carrier.
Specialized engineer pods : Obish and Gaitori engineer pods can be equipped, in order to make up for their lack of power, with special features: increasing the time to take over by five seconds, they can take control of enemy ships. It is still useless unless either the target ship is immobilized with maybe a moor, or unless the opponent gives you the ship to even the odds.
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Once caalaklael, now Pallas Athene
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Athena, daughter and favorite of Zeus, half sister of Ares, goddess of wisdom and war