I guess this is more of a speculation thing, but I don't think a Civil War speculation thread even exists and at least here someone will read this idea.
I had this idea as a cliff hanger for issue like four or five.
As the war rages on, tensions get higher and higher. SHIELD responds by authorizing more drastic measures to be taken to capture the underground fighters. This peaks when Captain America makes the top of FBI's most wanted list. In desperation, Maria Hill authorizes deadly force in the capture of Captain America.
SHIELD engages in a raid on the Underground's safe house. They go in guns blazing and catch most people off guard. They use indiscriminate fire against the heros while they're scrammbling for cover. Meanwhile Wolverine, Captain America, and [person Cap cares a lot about, hence forth known as Casuality A because I can't think of someone Cap cares a lot about right now, but I'm sure they're out] run through the emergency exit to the safe house. A small group of SHIELD agents catch up with them and open fire on them. Wolverine and Cap dodge the fire with ease and disable the agents, but Casuality A isn't so lucky. She took several rounds to the chest and is dying quickly. She/He tells Cap with his/her final breath, "never stop fighting." Cap is grief stricken, but Wolverine snaps him out of it, and they keep running.
Next we see Cap and Wolverine in a dive bar three hundred miles away from the safehouse. Cap sits there watching a news report about the raid while Wolverine gets drunk. SHIELD says, "The raid went off without any problems and we able to capture all the fugitives present and we only wish Captain America had been among them. This is still a victory, though, and this certainly marks the beginning of the end for these vigilantes." SHIELD mentions Causality A's death as regretable and stresses that if the SHIELD agents hadn't been met with such fierce resistance his/her death could have been averted. The last page shows Cap turn to Wolverine and says, "How are we going to kill this b*tch?" Wolverine looks at him and says, "Glad to see you're in this thing to win."
End of the issue...