They actually addressed this in last night's Agents of SHIELD. Apparently Fury had Coulson (and the Koenig brothers) working on something called Theta Protocal over the past year and a big part of that was building a new Helicarrier in secret. I never really thought he was on the run with no resources, he was on the run but he's Nick Fury. The guy in the comics who always had a contingency plan for when his 4th contingency plan went to shit. He burned his ID and one tiny storage locker filled with guns at the end of Winter Soldier, I really never even considered that was the sum of all his resources.


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