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In the third season of DS9, the entire station's compliment of commanding officers leave for the Gamma Quadrant. I do not believe this is an isolated incident, there seem to be several times throughout the series when the command officers are all absent from the station.

So who is in charge back on Deep Space Nine when this happens?

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Perhaps the attention-seeking "puppy" program was let out of its doghouse? (from 1x17, The Forsaken) – Izkata Jan 20 '13 at 5:17
Whomever is next in the chain of command? – CamelBlues Jan 20 '13 at 18:01
@CamelBlues which is who? DS9 has significantly fewer officers and personnel in general. It seems like all of the officers went to the Gamma Quadrant. – Jack B Nimble Jan 21 '13 at 2:00
There was no one else. In the event that Quark wasn't with them, then he was left in charge. If Quark was with them, then Rom was left in charge. – Xantec Feb 19 '13 at 21:57
I'd take Bajoran Security officer #3 over Rom any day of the Bajoran week. – Jack B Nimble Feb 19 '13 at 22:02
up vote 12 down vote accepted

I always thought Michael Eddington was left in charge.

I don't remember seeing him on the Defiant, and he was head of security...

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That makes sense; he was introduced in the previous episode, perhaps to close this very plot hole. – Matt Peterson Jan 21 '13 at 17:32

My guess would be that the night shift command officer was left in charge, or perhaps a Bajoran officer other than Kira. There is very little attention paid to the other shifts in most Star Trek series. Sometimes some of the books give them some attention. For instance we learn that Chekov was the night watch officer on Enterprise during the first season of TOS. But those aren't generally given the blessing of canon in the Star Trek universe.

The point is that there are likely numerous officers, both Starfleet and Bajoran on Deep Space Nine that we never hear anything about, any one of which could be left in charge in case the primary crew is absent, asleep or incapacitated.

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If ODO remained on DS9 then I think he would be in charge.he held the rank of CONSTABLE and I beieved he was head of security.

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Constable isn't a rank, it's a civilian position. And on a joint Starfleet/Bajoran military installation, his rank wouldn't count for anything in the chain of command. – Valorum Jun 18 at 19:16

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