So at some point I disassembled the transponder after finding all nodes. I've been back to both Sloane and the unlocked room to no avail. I can meet the contact at the Farm to start ZH, but don't want to start the missions if I can't get the rifle ultimately.
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I’m pretty sure that the transponder only unlocks the zero hour mission, and completing zero hour gives you outbreak perfected whether you have the quest or not. I could be wrong though.