Children's Crusade takes place close to the events of Deus Ex: Mankind Divided. The plot of the first issue is summarized as follows:
"With society still reeling from the Aug Incident - the Illuminati orchestrated event which caused augmented individuals to mindlessly attack their 'natural' counterparts - anti-aug sentiment is at an all-time global high. Task Force 29 - an Interpol-funded coalition, created to quash the rising tide of terrorist activity - stands as the world’s main defence against total anarchy.
In the city of Prague, where tension is especially high, the team’s latest recruit, Adam Jensen, readies for his first mission with the unit. But being augmented himself, how will the former SWAT officer handle himself when faced with the grim reality of the mechanical apartheid?"
"Following the first issue’s explosive revelation, Adam Jensen and TF29’s investigation leads them into the heart of the Glasshütte; Dresden's heaving transhuman ghetto, where the augmented struggle daily for basic survival. But with its residents, the media, and even the local police vying against them, it's going to be far from a clean-cut operation."
"Titus King's hate-mongering leads to escalating tension around TF29 HQ, leaving the strike force in an uncompromising position. Meanwhile, Jensen discovers a shocking new link to the pro-aug terrorists."
"As TF29 heads into the Glasshutte for a final confrontation with the pro-aug forces, two questions remain in Adam Jensen's mind: what will this mean for the future of augmentation and will the real conspirators ever come to light?"