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In the Stargate: Atlantis second season premiere "The Siege, Part III", Sheppard says about Ford:

It doesn't matter where he goes. The second he gets to wherever he's going, he's gonna ditch the Jumper, turn around, and dial another address — one we can't trace.

Why would Ford ditch the Jumper? It provides shelter, stealth mode, and the ability to fly. As for tracing gate destinations I'd have thought that, if anything, addresses dialled by a jumper are harder to forensically recover than addresses dialled on the gate's own DHD.

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There are economies of scale here which are implied, but never expressly stated. For example, you may also ask the entirely equivalent question,

During The Siege, why don't they just fly up cloaked in all the Jumpers, blow up the Hives with their combined drones (similar to what we see against the asteroid field in S4 prem or S3 ending), and then cloak again when not shooting? Even if they can't fire enough drones to kill a Hive, they could at least take out a large number of darts/blow up the launch bays.

The simple answer is that cloaking a Jumper has a non-trivial cost, which is never stated, but the character's suggestions regarding it imply it. In addition, it's clearly stated that Ancient cloaks and Ancient shields are very similar technology, and Rodney clearly states in 2x09 that they are not intended for long-term operation. The regular Jumpers are all brought back to Atlantis for servicing, recharging and whatnot, but Ford's never will be.

It's one thing to sit in a cloaked Jumper for a few hours, but the show never as far as I can see suggests using it for more than a few hours, and never suggests any tactic which would depend on more than this. In addition, the episode where Rodney gets sunk under the Lantean sea states clearly that the Jumper has a decidedly finite power supply, which Ford has no way to replenish without Atlantis. This leads us to conclude that

  1. Ford has to abandon the Jumper eventually, since it will run out of power.
  2. Ford would have to continually babysit the Jumper watching it's sensors to determine when he needs to cloak and run- he can't just leave the cloak on for funsies. This would leave him no time to do anything else. If he doesn't, it's a giant "PLEASE FIND ME" sign.
  3. We remember from the premiere that the Wraith are especially concerned with destroying or using any Ancient technology. It would attract a lot of attention. Ford on his own, however, isn't even worth sending a dart to feed on- if he was even detected.

In short, on his own, Ford can easily hide in plain sight in a human colony on his own. But the Jumper is a liability- he can't depend on it, he can't really hide it, and it's a giant sign for his enemies, and his friends, to find him.

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    Excellent answer. I agree with everything here, except your supposed "equivalent question". That Atlantis didn't use its jumpers as a military unit in any way during the seige remains a complete mystery to me (especially as those drones can do quite a lot of damage to a hive in short order) and cannot be explained by any of the above rationale. – Lightness Races with Monica Feb 14 '13 at 20:21
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    Ford might also have had sufficient loyalty to the human cause to not take somewhat valuable resources without a substantial benefit to himself, so even just taking the Jumper through the first gate might have been less attractive. – Paul A. Clayton Feb 14 '13 at 20:37
  • @PaulA.Clayton: Also a good point. – Lightness Races with Monica Feb 14 '13 at 20:59
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    @PaulA: I'd also suggest that if the Wraith recovered the Jumper, they may be able to find that it came from Atlantis after it's supposed destruction. – DeadMG Feb 14 '13 at 21:43
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    @LightnessRacesinOrbit Regarding your comment on the "equivalent question", they did attempt to fight off some incoming Wraith fighters and were quickly (and ridiculously) dispatched. Also, a key plot point in the asteroid episode was the gene treatment and training of personnel in operating the jumpers. Perhaps they simply didn't have enough people to fly them in the siege. – Chad Levy Mar 21 '13 at 19:21

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