In a flashback it is revealed that Wolverine saved Nick Fury's life. Why is this so important? Because it means that S.H.I.E.L.D. will throw in with the X-Men and not with Weapon X.
With Wolverine captured, the situation looks dire for the mutant prisoners of Weapon X but Wolverine reveals that it is all according to his plan.
The strain between S.H.I.E.L.D. and Weapon X comes to a boiling point when Colonel Wraith kills General Ross and some top commanders. Before this, it is revealed that the government is indeed planning to shut down Weapon X in favor of the Super Soldier Serum program.
Back to Weapon X, Sabretooth taunts Wolverine by destroying a dossier containing the truth about Logan's past.
Unfortunately, the dossier is destroyed. Why is this so important to Wolverine? Because of stuff like this:
Logan effectively does not know who he was.
As the issue closes, Logan's plan is revealed. He has allowed himself to be a living transmitter to call in the cavalry. And who is the "cavalry"? Why, it's the Brotherhood of Mutants.
It's a bit bothersome that the Blob is still eating. Hello man? You're in the middle of a mission.