This story starts off with an alien fleet attacking a human spacecraft or fleet - the alien fleet overwhelms their human counterparts, and destroy all the ships. A few survivors escape in individual survival pods, which the alien fleet starts to destroy - one of the survivors realises the aliens are using the pods emergency beacons to track the pods, so he disables his pods beacon and is instead taken aboard the alien ship as a prisoner.
He is kept in captivity for the remainder of the book, where we get an insight into the alien race.
The second stream in this book is from ground forces holed up on an alien planet, surrounded by alien forces. The human forces have taken refuge in amongst some buildings or structures which contain shelves of small sticks of meat or flesh, and it is assumed that this is a burial place. The human soldiers also report seeing alien ghosts amongst these buildings.
The reveal is:
The structures hold the respected elders of the alien race, who are susceptible to electromagnetic emissions, and the original attack was the result of a misunderstanding and response to the humans welcome messages.
This might be part of a series.
I read this in the 1990s.
Answer
This is the Conqueror's Saga by Timothy Zahn.
The first book, Conqueror's Pride has a battle as you describe, where after defeating the human ships, the Zhirrzh begin systematically eliminating the escape pods.
Commander Pheylan Cavanagh of the Kinshasa realizes, as he watches the Zhirrzh systematically fry the escape pods, that they are probably using the rescue beacons to target them, and destroys his to stop it transmitting.
And with a jolt of horror Pheylan understood. The aliens were firing on the honeycomb pods. Systematically and painstakingly destroying the survivors of the battle.
He swore viciously under his breath. The pods were no threat to the aliens--they weren't armed, armored, or even equipped with drives. To destroy them like this was to turn a military victory into a cold-blooded slaughter.
And there was nothing that he could do about it except sit here and watch it happen. The pod was little more than a minuscule cone with a power supply, a dioxide/oxygen converter, a backup oxygen tank, an emergency radio beacon, a short-range comm laser, two weeks' worth of rations, a waste-reclaimant system--
He was clawing the equipment access panel open almost before the thought had completely formed in his mind. The aliens out there weren't just blasting every chunk of rubble in sight; they were specifically and deliberately hunting down the pods. And suddenly it was blindingly obvious how they were doing that.
The emergency beacon was a deliberately simple gadget, as unbreakable and foolproof as anything in the Peacekeepers' inventory. But foolproof didn't necessarily mean sabotage proof. A minute later, every wire and circuit line to it cut and the blade of his multitool jabbed into its internal power backup, it had finally been silenced.
We later learn that, from the Zhirrzh point of view, radio broadcasts are called "elder death weapons" and it was the elders on the first ships who called for the attack on the human ships. They perceived the human attempts to communicate (by radio broadcast) as an attack, and the continued radio transmissions from the beacons on the escape pods were the reason for destroying them.
Silencing his beacon is enough to keep Commander Cavanagh from being destroyed but not enough to hide him from them, and he is captured and taken aboard a Zhirrzh ship.
Now if he could just make it outside the cone of whatever focused sensor beams the aliens were using...
Concentrating on the first ship, he never even saw the second ship's approach. Not until the blue light abruptly flared around him.
Commander Cavanagh is kept prisoner until late in the novel when a privately-organized search-and-rescue party finds and recovers him. (Lord Stewart Cavanagh, Commander Cavanagh's father, is an ex-parliamentarian - "Parlimin" - with military contacts he uses to organize the rescue force.)
The Zhirrzh have a special organ (the fsss) that is extracted at death, and from which the animus of the departed Zhirrzh (the "elder") is able to manifest and communicate with the living. It is possible to divide this organ in two, so that the elder can manifest in either of 2 places. By placing groups of dozens to a few hundred of these in places, they can create a faster-than-light communication system where messages are routed among the elders. It is also how early-warning systems are constructed, such as the one found by the human ground forces.
"I see." Holloway picked up a small plastic sample box from the scattered electronic equipment and stacks of paper cluttering the desk and handed it to her. "Take a look. Tell me what you think."
Melinda took the box and looked through the lid. Inside, nestled in the palm of a camouflaged glove, was a thin, dark-brown disk, slightly curled at the edges. "It looks like a slice of sausage," she said. "Where did it come from?"
Holloway gestured to the camouflaged men. "Sergeant Janovetz?"
"We found it just north of the settlement," a raw-boned man near the middle of the group said. "In a little cubbyhole built into a sort of white pyramid thing the Conquerors have got set up on Overview Ridge."
Melinda frowned at Holloway. It had been barely two days since the Conquerors had invaded. "They're moving equipment in already?"
"They moved these in, anyway," Holloway said. "There appear to be four of them: one each north, south, east, and west of the settlement."
The elders are occasionally visible to the humans, keeping them under surveillance, and the humans see them as "ghosts." The first time this happens is when Melinda Cavanagh is examining the disk described above:
Turning away, she lifted her gloved hand to the seal on the breather mask—
And froze. There, no more than ten meters away, something was floating slowly through the air across the storage area. Something pale white in color, insubstantial in form, moving between the piles of boxes and equipment.
A ghost.
Against her cheek Melinda felt her hands begin to tremble, every ghost story Aric and Pheylan had inflicted on her as a child surging back in a bubbling flood of panic. She took an involuntary step backward, coming up short as the small of her back rammed into the cold storage box. The ghostly figure paused, seemed to turn its head toward her—
And with a flash of horror she saw that the face turned toward her was that of a Conqueror.
It vanished at that moment, disappearing instantly into nothingness. But it didn't matter. Melinda's scream was already on its way.
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