MCR frontman Gerard Way told Billboard:

“S/C/A/R/E/C/R/O/W” was a really amazing moment. It was, again, the band doing songs for the sake of making great music. We really wanted to explore the psychedelic nature of this album. We had started to think of it as this thrashy, Magical Mystery Tour kind of this album. It didn’t have a story or a concept, but it had this high concept that it had all this color.

“S/C/A/R/E/C/R/O/W' was the art piece, and where the album really started to flourish.

It’s likely that this story is told from the Killjoys' point of view! In MCR’s fictional universe, the Killjoys are on the constant run from the government industry, BLI.

Workers for BLI are often referred to as scarecrows – people who do the work for the others, but are brainless in themselves. The chorus refers to hiding at night, and staying on the run. It could alternatively refer to hiding the dead from the government so that the Phoenix Witch can take them to their next life, as explained in the comics by Cola.