I think the answer is...
Long ago, my militant leader devised a plan for world domination
Scooping up whatever organic molecules he could, this leader figured out a way to replicate himself, build armour, and weapons, to coldly dominate with copies of himself.
Though he is now gone, I am still carrying out his plan
Evolution marches on. Genes are replicating entities within the larger replicating structure of DNA. All of which is a distant descendant of that original replicating 'leader', but that specific replicator is long gone, probably consumed by some of his stronger descendants. Genes now carry out the same plan.
Today, our territory is near second to none
We construct our survival machines all over the world, pretty-much.
Many have died for me to live
"The secrets of evolution are time, and death." - Carl Sagan. Genes would not be where they are today without death.
And I am well seasoned, but there are times when my armor does fall away
Genes are usually very well adapted to influencing whatever physical and behavioural traits benefit themselves. However, mutation (in themselves or other influencing genes) often prevents them from being passed on in particular hosts (the living things they build in order to replicate down the generations). Extinction also fits this clue as it stops a line of genes, whereas mutation would only affect one line... his identical counterparts would still be passed on in others.
I have secrets of my own, but you must know me before you could begin know them
Oh, the secrets in DNA and our genes! The general public have an awareness of these, but only those who study genetic material and really have a good understanding of it can hope to uncover some of the unknown secrets they hold.