The issue really laid the groundwork for a split between S.H.I.E.L.D. and the Ultimates (Ultimate Avengers) at the conclusion of Millar's run.
Fury no longer has faith in the big three (Captain America, Iron Man, and Thor) and isn't too fond of any of the others either. Tony Stark is busy designing and building technology independently that has the U.S. govt. nervous. For one of the biggest missions imaginable, Fury decides to go with the Reserves instead of the Ultimates, and they (the Reserves) better fit Fury's desire for a superpowered military team anyway.
Even if Steve Rogers is proven innocent (which you have to assume will be the case), too much has taken place for the Ultimates to simply reunite with Fury under S.H.I.E.L.D. command at this point.
Fury no longer has faith in the big three (Captain America, Iron Man, and Thor) and isn't too fond of any of the others either. Tony Stark is busy designing and building technology independently that has the U.S. govt. nervous. For one of the biggest missions imaginable, Fury decides to go with the Reserves instead of the Ultimates, and they (the Reserves) better fit Fury's desire for a superpowered military team anyway.
Even if Steve Rogers is proven innocent (which you have to assume will be the case), too much has taken place for the Ultimates to simply reunite with Fury under S.H.I.E.L.D. command at this point.