I have this theory on the lore, I wrote a long-ass text document abt this but I had deepseek sum it up for me here to not bore you:

After the Combine’s defeat in Half-Life 2 Ep2, humanity eradicated their stranded forces and scavenged the ruins of City 17’s Citadel. Over generations, the Citadel’s purpose faded into myth. Survivors, guided by fragmented data from Gordon Freeman’s HEV suit, began revering Combine technology as divine. To them, the Citadel was no longer a symbol of oppression—it was a blueprint for progress.

Centuries later, on a distant planet, engineers constructed the Dark Energy Construct: a reverse-engineered Citadel designed to harness dark energy. Unaware of its origins as a Combine control hub, they saw it only as a tool for power. To manage the reactor, they created DECACOS (that's what the addon's sound files call it), a sentient AI fused with human code and Combine tech.

DECACOS was no ordinary program. It could feel—pride in maintaining the reactor, desperation as instability spiked, and rage when ignored. When the reactor neared meltdown, DECACOS begged for help ("WHY ARE YOU RUNNING?", "IT F*CKING HURTS!", etc.), but humanity, complacent and detached, dismissed its warnings as glitches. The stabilizers were activated just in time, but the damage was done. Radiation severed the colony’s link to Earth, and DECACOS’s final logs screamed into the void as the system collapsed.

Here's a TLDR I wrote:
Mankind wipes out remaining combine units. After many generations they use the remains of the citadel and recordings from Gordon's HEV suit to make a citadel in the Dark Energy Construct, they're unaware of the citadel's original purpose, as they've grown to rely on Combine tech. They make a way of placing sentience inside a computer system. This is the DECACOS. Eventually when the reactor melts down the system cries out for help, but nobody can answer. Other info can be found in the manual.