What is the meaning of the lyrics to Coheed & Cambria's song, "In Keeping Secrets of Silent Earth 3"?

There were many events and introduced characters to get to this point (from Coheed's first CD, The Second Stage Turbine Blade) but I'll try to sum up the relevant stuff and a bit of the context. So, as stated above, this song is about Claudio Kilgannon's dreams as he lays asleep in hiding on Shylos 10, the planet the Red Army uses for its torturous interrogations. The events in this war actually happen but here are described in Claudio's dreams (probably an after-effect of his being the son of Cambria, "The Knowledge", who has psychic visions).

Jesse and the IRO-Bots he has created, his "children" engineered as powerful weapons, confront the Red Army on Silent Earth. They are terribly outnumbered yet desperately fight on as time passes (A broad incision sits across the evening/The victim to our father's lost war). Some of the IRO-Bots question their fate (restless children sit and mourn the graves) and wonder "Will they be buried here among the dead?"

These chosen fighters --previous weaker versions of them were incinerated by Jesse-- are the "pioneers" who have to be dealt with by General Mayo and his marching army along with any uprising or support for rebel Mariah, the Secret, a new mage immaculately conceived and possessing healing powers (The pioneers/ In dealing with it they march for dawn, of Will[helm] and worthy/The truth be told the child was born!). Mayo urges his army onward and taunts his opposition (Man your own jackhammer[a laser cannon-like weapon]/Man your battle stations/ We'll have you dead pretty soon).

One of the children, later referred to as Sizer, has had recurring jealously toward his "sister" Chase because Jesse appears to favor her. His childish envy/desire for approval bursts forth in this war (Jealous envy for the youngest one/To be the hero is all I'll ask/Can I be buried here among the dead?) and he vows to gain Jesse's love and glory even if it kills him. He reiterates his desperate desire for parental approval --at any cost-- with, "For you,
I'd do anything just to make you happy, hear you tell me that you’re proud of me/For them, I'll kill anything cut the throats of babies for them break their hearts for they were them/Waiting for you to say: I love you too". This foreshadows his act of giving up himself up to the Red Army in exchange for captured Chase in the next song, Cuts Marked in the March of Men (deliver a favor to my [Jesse's] love [Chase], and Sizer does) and leads to his subsequent torture in Three Evils.

THe IRO-Bots continue battling and Jesse laments the suffering caused by Willhem Ryan (supreme dictator of their universe and Mayo's superior)-- "Will, Do the children really understand the things you did to them?". Jesse's army appears to be in bad shape, with the tide of battle turned against them, and he considers their imminent defeat (we're coming home pretty soon/Coming home) with home as a metaphor for death. Still he appreciates the sacrifice of their efforts, united completely even in such dire straits against the threat to their world (We were one among the fence/One among the fence [Heaven's Fence is their universe]).

At the end Mayo confirms that Jesse and his children are indeed nearing defeat with a repetition of the taunting refrain along with "Man your battle stations/ We'll have you home pretty soon--tonight".