I feel sure this has been hashed over already, but I feel compelled to add my irritation with the game automatically choosing which fleet I am attacking, and then not being able to stand down when the fleet it chooses is my ally, rather than our mutual enemy.

Most recently, during the second phase of the Load Stone quest, my ally entered the system with 9 ships without a single gun on them, and our mutual enemy arrived in the same turn, with a siingle well armed warship. 

I'm guessing the game chose my ally because they had more ships, rather than our enemy because it had more hitpoints.

Isn't that kind of like defending yourself during a RW armed robbery, by attacking the little old lady with a dozen bannanas rather than the robber with only six bullets?

I'm not here to complain though, but only to request a 'Stand Down' button during the initial attack screen, or even better, the ability to pick the fleet I want to attack.

Let us not also forget how nice it would be, if I could defend my transport fleets by having an option of forcing the AI to fight through my fleet of warships in the same system as the transports they destroyed.

Thanks

was your ally ACTUALLY in an alliance with you? or even at Peace?

pretty sure if they were then that's a bug you've found.

Yes, we are/were in an alliance.

I assumed I would attack the enemy ship and clicked the crossed swords, the game pitted me against my allies unarmed ships and so I chose to retreat. 

The result was that all of our ships were destroyed.

I'll take it to the Bug report forum and include the save game file.

Either way though, I still want the 'Stand Down' button and an option to choose for offence and defence.

You can already choose which fleet you attack if you're attacking on a node with multiple enemies. If you're in the Academy Quest, the Special Nodes put all prior alliances on hold. You're only able to attack Empires that chose the opposite side of the conflict as you, regardless of other diplomatic relations. If you want to attack an enemy fleet even when they're chosen the same philosophical side in the grand galactic debate, it can't be on one of the Lodestone systems, you gotta take your guns elsewhere. Likewise, if you're in an alliance with someone, but they're in favor of awakening the old gods while you chose to double-tap them back into the grave, you can slap each other around on the Lodestones with impunity.

Basically, check the symbol next to the fleet icon. If you and your enemy have a yellow triangle while your ally has a blue beaker or vice versa, for the purposes of the Lodestone, you've switched teams. If you're concerned about things happening outside of the quest, keep your primary fleets off of the nodes.

Yeah the lodestone quest can really throw you off if your allies choose the other team...and the AI WILL do it just to screw you over.  Anywhere else, you're allies, but on that lodestone system, your quest team is all that matters.