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They didn't need Rodney's code for the self destruct, just the alert beacon. The computers shut down before Sheppard could shut down the self destruct. Also, it makes since to not give Sheppard the quarantine Shutdown code since A: He is no longer the military commander on the base and B: Remember the last time Atlantis got quarantined? He breached it in direct conflict with an order from the base commander.
Very good point. Poor Shep didn't realise he'd been demoted But definitely too naughty to have the quarantine codes!
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