If it was attacking your system shouldn't you have won when the time ended? That's how Total War works, defender wins on timeout.
In a
normal fight, say, between two player fleets, both sides retreat, remain at the same location and will fight again(if they don't move somewhere else) next turn. I'm not sure what happens if you fail to kill a silicoid queen in time, maybe it establishes itself as a hive.
Puppet Master will mind-control the entire star system.
EDIT: I finally figured out how to switch the Titan Compact(which fires AT missiles) to top-attack mode, in which the missiles fly up, then hit the target on top(like a Javelin, which the Titan is
not based on). This was during an AAF attack on Negades, which is odd since I thought there was a range limit from your HQ for attack missions to be generated and my HQ is halfway across the map now. Anyhow, attack's over before I can get there("halfway across the map now"), Negades flips, and I set up for at least damaging the attack force at the (still destroyed) radio tower on the mountaintop south of Negades, bringing a full squad and a truck with both Titan models and ammo for both.
Helicopters strafe the tower base. Nobody's hurt, either here or the power plant south of the tower. I was preparing for tanks, so I didn't have the AA launcher ready, and so I didn't get any hits in. I don't know how many helicopters got shot down, definitely one for sure. There were probably some ground forces somewhere south of the power plant, since the mortars at the tower outpost start firing and don't stop. I drive over to a cliff overlooking Negades, spot some AAF infantry hanging around, get my squad lined up to fire down.
Then I see an APC, and I can't lock on it from my position. It rams a civilian truck, exploding it, and a minute later starts driving away, giving me the line-of-sight to establish missile lock. First hit doesn't kill, and neither does the PCML rocket one of my AT guys fires almost simultaneously. The top-attack missile hit must have disabled the APC's turret however, since it didn't immediately instantly murder
my squad me. Another Titan missile
levels an entire city block along with the APC. Almost immediately: "Task completed: Negades joins FIA."
Arma 3: Antistasi. Normally, collateral damage generally loses support from the town whose insurance premiums you increase, but it's possible that it was the APC exploding that destroyed the buildings, causing the game to assign the blame to APC, losing support because it's their fault for being attacked.
Also running into an annoying bug where static objects placed by me don't have their positions correctly saved, being saved with coordinates a few paces to the east of where they're actually placed. As a result, I've got an AA launcher blocked by a car wreck, and a concrete bunker that's slowly migrating out to sea.