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In the last act of Captain America: The Winter Soldier, this conversation is exchanged.

[Computer] Retinal scanner active.

[Alexander Pierce] You don't think we've wiped your clearance from the system?

[Nick Fury] I know you erased my password. Probably deleted my retinal scan. But if you want to stay ahead of me, Mr. Secretary, you need to keep both eyes open.

What did Fury mean by both eyes open? A simple mention that he doesn't trust anyone, so you have to pay attention to your friends and enemies, or is there something deeper?

If SHIELD deleted Nick Fury from the database why would his blind eye still have security clearance?

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    Keep both eyes open is a play on words. He means as you said: Don't trust anyone and keep your eyes open. But it's also a joke because he doesn't have two eyes to open. But it's also the reveal that although it's behind an eyepatch and could be forgotten about, it's still an eyes that apparently also has a retinal scan. – IronSean Apr 30 '18 at 17:31
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Nick Fury is a far-sighted fellow, and presumably prepared for this contingency by creating an entirely separate and secret superuser account using his blind eye, which wasn't deleted because no one in Hydra knew it existed.

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    Do you have any evidence for this or is it entirely speculation, albeit informed? – TheLethalCarrot Apr 30 '18 at 14:38
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    The evidence is in exactly what we saw and what was said. Pierce stated they wiped him from the system. Nick Fury himself says he fully expected that, and yet he gains access anyways, with a retinal scan from his blind eye instead of his usual one. He also makes statement to the effect of "I counted on this happening, and gave myself a backup way in". Short of someone actually bothering to explain all the details in "villainous plan monologue" fashion, the scene seems to play out pretty straightforward in what happened. – Mwr247 Apr 30 '18 at 15:08
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    Great Scott! An excellent pun sir. – Lightness Races in Orbit Apr 30 '18 at 17:57
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    Nice. Also, per the "entirely separate and secret superuser account using his blind eye", this would commonly be referred to as a "backdoor" for those interested in the general idea. And I would assume that for most users trying to access the system, removing access involves checking for the retinal fingerprint of both eyes, and that in this case, the SHEILD sysadmins simply neglected to do this for Nick Fury, thus making his "you need to keep both eyes open." comment a wink (get it!) to their oversight. – Anthony Apr 30 '18 at 19:07
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    @Anthony It might not; it could be an implanted pattern on the eye (so it doesn't even look like a retina scan) or a false eye with a printed out backdoor on it. It could even be a buffer overflow style exploit. – Yakk May 1 '18 at 14:57

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