Okyo brings a baby to the school. She was handed the baby by a stranger on the street. He was being pursued by somebody. Also being an orphan, Saki feels compassionate about this matter and tries to find the baby's parents.
Saki gets her next mission and it is to search for Itazaki, a specialist in military science. Meanwhile, Okyo and the baby disappear.
In fact, Seirokai wants to utilize Itazaki's knowledge and to persuade him, they kidnapped his son, who happens to be the baby that Okyo is with.
Threatened by Seirokai, Itazaki agrees to program a plan to kill Saki.
According to the plan, Saki and Yukino are lured to a military laboratory and encounter various traps, which they barely escape. They succeed reuniting Itazaki and his son.