With most of the introductions out of the way, Gunslinger Girl delves into the nitty-gritty of the different jobs that Henrietta and her young comrades must undertake. Sticking with the single episode-per-story format, GG vol. 2 spends the first 2 episodes following the girls on missions, and the last two focusing on two of the lesser-known girls.

The first pits Henrietta and her handler, Jose, against an arrogant explosives specialist who seems to have no other purpose in life than to simply blow stuff up. Called in as extra help by a friend on the police force, Jose decides that a single Fratello may not be enough to ensure the mission's success. Feeling at first somewhat sulky about Jose's decision to bring in more help, Henrietta later realizes that having to work with the other girls is not necessarily a lack of faith in her abilities.

In the second episode, it's Rico's time to shine as the story now focuses on her. Rico and Jean, posing as father and daughter on a leisurely trip to a famous museum, run into a friendly middle aged man who ends up showing the Fratello around the city. Half way through their sightseeing expedition the party is attacked and Rico's true purpose as protection for this strange art-loving man is revealed. Rico once again shows that although she has to deal with Jean's tough and unforgiving method of handling, she still has a good heart and only wants to do her best for him.

The spotlight then switches yet again to tell us about Angelica, an up til now, mostly background character. Although she is seen briefly in previous episodes and she has been at the agency almost from the beginning, little to nothing has been told about how she came to be where she is. Before coming to the Agency, Angelica was a victim of a vicious hit and run by her own parents and left to die. Post surgery and conditioning, Angelica and her handler Marco shared a relationship similar to the one Henrietta enjoys with Jose. And things were good. However, one day it becomes suddenly and painfully apparent that Angelica is rapidly losing her memory. Bitter, horrified and terribly discouraged by this sad side effect of her conditioning, Marco violently rejects her. Somehow he must come to understand that abandoning Angelica when she needs him most is perhaps the worst thing he can do to her.

Last of all, Vol. 2 introduces the newest girl at the Agency, Elsa. Although no background information is given on the new girl, her mission with Henrietta turns out to be very telling about the quality of her life. Elsa is a severe work-absorbed introvert. She does not fraternize with the other girls and she is stand-offish at the best of times. When Elsa's handler, Lauro, requests Jose's help on an upcoming job, Henrietta is thrust into a co-op mission with the unsociable girl. In a fruitless attempt to be friendly, Henrieta visits Elsa the evening before the job. However, her friendly overtures are rudely rebuffed and Henrietta gives up on ever making a friend out of Elsa. In transit to the mission site, it becomes very apparent that Elsa envies Henrietta's relationship with Jose, and attempts to get something more out of Lauro than responses one would give an obedient work horse. Lauro has no love or respect for his girl, and really doesn't understand why anyone would waste kindness on a cyborg.

There is no appreciable change in Gunslinger Girl's storytelling from the first disc. So expect even more emphasis on the personal relationships than the actual missions themselves. In fact the missions are almost inconsequential and are used really only as vehicles for the growth and maturation of the girl assassins. Henrietta is an excellent example, as her confidence in her abilities, her place, and her relationship with Jose are definitely on the rise. Rico and Elsa both expose the gap between the training styles of handlers like Jose and handlers like Lauro and Jean. And it's hinted that these types of negative and positive reinforcement styles will ultimately determine the usefulness and longevity of the girls. Both Lauro and Jean will have no one to blame for their broken "tools" but themselves.