Cold atmospheric plasma is an emerging technology in the treatment of cancer. Meanwhile, different types of self-organized pattern (SOP) phenomenon have been reported in a wide of range of plasmas. In this paper, we describe the application of SOP plasma to two breast cancer cells MDA-MB-231 and MCF-7. Specifically, the effect of SOP plasma on reactive oxygen and nitrogen species (RONS) were investigated. SOP plasma-generated RONS displayed significantly decreased cancer cell viability in both breast cancer cell lines; significantly inhibiting cell proliferation via while inducing apoptosis. SOP plasma induced DNA damage, activating the ATM/ATR kinase signaling cascade. ATR phosphorylates the checkpoint effector kinase Chk-1 activating γ-H2AX resulting in cell cycle arrest and ATM induced apoptosis. Taken together, we have provided new insight into the action mechanism of action by which elevated SOP plasma first induces ROS generation and then results into a DNA damage response, ultimately inducing apoptosis.