The Seer, about 23 minutes in (of course I didn't use this as an excuse to re-watch season 4 *g*): Carter comes in and asks Rodney about what progress he's been making with the shut-down code and he says it's "not very promising" The gist of it is that switching on the attack code was relatively easy, because that's what the Replicators were designed to do, but switching them off is virtually impossible without the original Wraith virus - which they plan to obtain from Todd. Todd's ship transfers the virus, and Todd and McKay work on it together, but Rodney figures out it's incomplete. It was Todd's insurance policy: give them just enough to almost finish it, but keep some back so they have to keep him alive. They have to put the kibosh on that plan when Todd's hive ship is destroyed
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The gist of it is that switching on the attack code was relatively easy, because that's what the Replicators were designed to do, but switching them off is virtually impossible without the original Wraith virus - which they plan to obtain from Todd. Todd's ship transfers the virus, and Todd and McKay work on it together, but Rodney figures out it's incomplete. It was Todd's insurance policy: give them just enough to almost finish it, but keep some back so they have to keep him alive. They have to put the kibosh on that plan when Todd's hive ship is destroyed