Ms. Marvel begins her career as the leader of the Initiative strike team Operation: Lightning Force by battling A.I.M. leader MODOK.
MODOK’s faction of AIM is trying to steal a DNA bomb from another branch led by the “scientist supreme.”
Ms. Marvel’s team stops them. Along the way, we get a solid Wonder Man vs. Ms. Marvel fight when MODOK is able to mind-control Simon.
At the same time, across these issues it appears that the two heroes are sleeping with each other.
I’m pretty sure those two civilians are supposed to be Brian Reed and Aaron Lopresti.
Scientist Supreme is able to get the DNA bomb implanted in MODOK’s head and blow it up in Times Square, and Ms. Marvel absorbs all of its power to save innocents. This temporarily mutates Ms. Marvel and may in fact have altered her DNA.
Complicating all of this: MODOK’s own son works for AIM and is on the side of the Scientist Supreme. He is the one who bomb-ifies his own father’s head. At the end of the story, we see that he has now been transformed into the new villain, “Head Case.”
As for daddy MODOK, his whereabouts are unknown and his body was not recovered at the scene of the explosion.