When I read "have the target in custody" I take that quite literally. You're cutting to the moment where the cuffs have been slapped on the character's wrists.
Now the trick is "How do the PCs get out with this guy?"
Admittedly, I run Age of Rebellion, so if the PCs decide they want to take out an Imperial Officer, it's very likely the PCs will find themselves in the middle of a heavily fortified Imperial Compound, teaming with more Stormtroopers than you'd functionally need to count.
Also note that they can track an NPC if they know what planet that NPC is on. I have an easier time of this, because a lot of the officers in my game tend to be stationed aboard their flagship... Technically, this means they are not on a planet. That seems like a bit of a loophole, but it also makes a certain amount of sense: Infiltrating a ship is a lot harder than infiltrating a facility groundside.
With that said, though, for certain really pivotal NPCs, I tend to apply their adversary Rating to any signature abilities that target them. And I'll also throw in setback dice depending on various factors, such as, "They are in a heavily fortified facility," or "they have a lot of bodyguards" or, "They're pretty central to the plot, so I'm not gonna make this easy on you." (That last one is more of a silent factor that I use to inflate other "reasons" to add setback dice)
Still, when the PCs have really solid dice pools, even a mountain of setback dice isn't necessarily a great defence. And on those occasions, I have the hostage be more trouble than they're worth. Hidden tracking devices, lockpicks, tempting bribes, other people looking for the same bounty. There's lots of ways to screw with the PCs on the way back from the mission, too.

I'm getting 404 errors off all the links. Have these been taken down?

I draw a lot of inspiration for Age of Rebellion from the old TIE Fighter game. Not necessarily canon, but it sets a certain tone. I use the greek alphabet to designate Imperial fighter groups, The Secret Order of the Emperor goes around giving people weird tattoos and cryptic missions, and the briefing is always given by the same briefing officer.
I do want to run a Resistance Era campaign (I quite like the sequels), but I can definitely wait for the sourcebook. 
Personally, I never felt like Stormtroopers were *super* elite. They're a cut above Imperial Army, sure, but they also weren't terribly rare, even in the old canon. When I think elite troops, I think Storm Commandos and Death Troopers. This "Elite Stormtrooper" nonsense strikes me as Imperial propaganda. They want Stormtroopers as a symbol of oppression, and if the people believe they're all fanatically loyal and expertly trained, then people are a lot less likely to challenge the faceless symbols of your rule.
But they're just dudes with guns and marginally better armour. They were never anything special.

I draw a lot of inspiration for Age of Rebellion from the old TIE Fighter game. Not necessarily canon, but it sets a certain tone. I use the greek alphabet to designate Imperial fighter groups, The Secret Order of the Emperor goes around giving people weird tattoos and cryptic missions, and the briefing is always given by the same briefing officer.
I do want to run a Resistance Era campaign (I quite like the sequels), but I can definitely wait for the sourcebook. 
Personally, I never felt like Stormtroopers were *super* elite. They're a cut above Imperial Army, sure, but they also weren't terribly rare, even in the old canon. When I think elite troops, I think Storm Commandos and Death Troopers. This "Elite Stormtrooper" nonsense strikes me as Imperial propaganda. They want Stormtroopers as a symbol of oppression, and if the people believe they're all fanatically loyal and expertly trained, then people are a lot less likely to challenge the faceless symbols of your rule.
But they're just dudes with guns and marginally better armour. They were never anything special.

I draw a lot of inspiration for Age of Rebellion from the old TIE Fighter game. Not necessarily canon, but it sets a certain tone. I use the greek alphabet to designate Imperial fighter groups, The Secret Order of the Emperor goes around giving people weird tattoos and cryptic missions, and the briefing is always given by the same briefing officer.
I do want to run a Resistance Era campaign (I quite like the sequels), but I can definitely wait for the sourcebook. 
Personally, I never felt like Stormtroopers were *super* elite. They're a cut above Imperial Army, sure, but they also weren't terribly rare, even in the old canon. When I think elite troops, I think Storm Commandos and Death Troopers. This "Elite Stormtrooper" nonsense strikes me as Imperial propaganda. They want Stormtroopers as a symbol of oppression, and if the people believe they're all fanatically loyal and expertly trained, then people are a lot less likely to challenge the faceless symbols of your rule.
But they're just dudes with guns and marginally better armour. They were never anything special.

I draw a lot of inspiration for Age of Rebellion from the old TIE Fighter game. Not necessarily canon, but it sets a certain tone. I use the greek alphabet to designate Imperial fighter groups, The Secret Order of the Emperor goes around giving people weird tattoos and cryptic missions, and the briefing is always given by the same briefing officer.
I do want to run a Resistance Era campaign (I quite like the sequels), but I can definitely wait for the sourcebook. 
Personally, I never felt like Stormtroopers were *super* elite. They're a cut above Imperial Army, sure, but they also weren't terribly rare, even in the old canon. When I think elite troops, I think Storm Commandos and Death Troopers. This "Elite Stormtrooper" nonsense strikes me as Imperial propaganda. They want Stormtroopers as a symbol of oppression, and if the people believe they're all fanatically loyal and expertly trained, then people are a lot less likely to challenge the faceless symbols of your rule.
But they're just dudes with guns and marginally better armour. They were never anything special.

I draw a lot of inspiration for Age of Rebellion from the old TIE Fighter game. Not necessarily canon, but it sets a certain tone. I use the greek alphabet to designate Imperial fighter groups, The Secret Order of the Emperor goes around giving people weird tattoos and cryptic missions, and the briefing is always given by the same briefing officer.
I do want to run a Resistance Era campaign (I quite like the sequels), but I can definitely wait for the sourcebook. 
Personally, I never felt like Stormtroopers were *super* elite. They're a cut above Imperial Army, sure, but they also weren't terribly rare, even in the old canon. When I think elite troops, I think Storm Commandos and Death Troopers. This "Elite Stormtrooper" nonsense strikes me as Imperial propaganda. They want Stormtroopers as a symbol of oppression, and if the people believe they're all fanatically loyal and expertly trained, then people are a lot less likely to challenge the faceless symbols of your rule.
But they're just dudes with guns and marginally better armour. They were never anything special.

My general solution is more stormtroopers. If I throw 5 minion groups of 4 at the party, you can only kill one of these groups per round. Still breezing through? More minions! Have more show up to replace the fallen in waves.
The Nebulon-B tends to be my go-to mid-tier Imperial vessel. A nebulon-B typically carries 72 troopers, which I generally divide into 5-man minion groups led by stormtrooper sergeants. You may win on single target damage, but the empire wins through sheer action economy.
My motto has always been “The Empire always has more stormtroopers” and it has yet to fail me.
Worst case scenario, I airdrop a couple AT-STs on you. I always have ways to escalate an encounter beyond the PCs abilities.

Fixed. Thanks for the heads up.
Took awhile to get around to it. Sorry about that!

I know it's not on topic, and far be it from me to judge your table because I've never GM'd something like this, but this seems to me to be, as Tony Stark would say "Not a great plan."
If I were a player I would be absolutely livid if my GM destroyed all my PC's forces that I had "grown to be close to" over the course of a campaign in a literally unwinnable charade, only to be rescued by a "retired" GMPC galloping in on a white horse to Save the Day (tm), all in order to reintroduce said GMPC and to drastically reroute the course of the campaign. I can tell you, even if it was in character for my PC to rejoin the GMPC and get back to square 1 freelancing, as a player, this would be my last mission of the campaign. 

Make the battle desperate, make the costs high, but a) give them an objective that makes the sacrifice worth it and b) let them win (or lose) on their own abilities.

I know it's hard not to make your GMPC the "Big **** Hero" (everyone wants to be the Hero) but you're shortchanging and disrespecting your players by doing so.

Also, incidentally, Battle of Jakku seems like a capstone to a campaign. Is there a particular reason you want to transition back from "The PC's lead thousands" to "guns for hire"? Wouldn't it be simpler (with less hard feelings and less leaps of logic) to make this the dramatic conclusion (wherever the dice fall), and to start afresh on a new freelancer campaign?

My general solution is more stormtroopers. If I throw 5 minion groups of 4 at the party, you can only kill one of these groups per round. Still breezing through? More minions! Have more show up to replace the fallen in waves.
The Nebulon-B tends to be my go-to mid-tier Imperial vessel. A nebulon-B typically carries 72 troopers, which I generally divide into 5-man minion groups led by stormtrooper sergeants. You may win on single target damage, but the empire wins through sheer action economy.
My motto has always been “The Empire always has more stormtroopers” and it has yet to fail me.
Worst case scenario, I airdrop a couple AT-STs on you. I always have ways to escalate an encounter beyond the PCs abilities.

Spotted a Typo in the Steel Hand Adept sheet. The 20 xp Toughness Talent lists +1 Wound Threshold, when it should list +2. 

I’m on board. The combo of anime-inspired visual styles and a focus on starfighter pilots gets the wheels turning on my head.
I suspect Gundam might be a good analogue, though probably not quite as grim in tone. Gundam is animated, but there’s still an emphasis on realism. Everything feels like it operates accordig to blueprints, characters may ham it up a but but won’t take absurb pratfalls or jump 20 feet in the air if you startle them, etc.
And, ****, I’d definitely watch a show like that. Actually...
 
 
Now, I’d probably go with a slightly brighter, cleaner art style, but I think this drives home the idea that “anime-influenced” can fit pretty comfortably within Star Wars without feeling out of place.
 

I’m on board. The combo of anime-inspired visual styles and a focus on starfighter pilots gets the wheels turning on my head.
I suspect Gundam might be a good analogue, though probably not quite as grim in tone. Gundam is animated, but there’s still an emphasis on realism. Everything feels like it operates accordig to blueprints, characters may ham it up a but but won’t take absurb pratfalls or jump 20 feet in the air if you startle them, etc.
And, ****, I’d definitely watch a show like that. Actually...
 
 
Now, I’d probably go with a slightly brighter, cleaner art style, but I think this drives home the idea that “anime-influenced” can fit pretty comfortably within Star Wars without feeling out of place.
 

I feel like, certainly in Edge of the Empire, characters are incentivised to not be combat specialists. If you’re not a bounty hunter or hired gun, you probably don’t have combat skills. That’s telling.
And Star Wars is full of examples of non-combat characters influencing combat. Look at R2. He’s always opening doors, throwing up smoke screens, etc.
I’m also a staunch believer that combat is a last resort in Star Wars. The empire always has more stormtroopers, so you better have a better plan than “stand and fight”. A nebulon-B frigate has 70 troopers at its disposal, and I will make you fight them all if you decide to make a stand rather than run.

I feel like, certainly in Edge of the Empire, characters are incentivised to not be combat specialists. If you’re not a bounty hunter or hired gun, you probably don’t have combat skills. That’s telling.
And Star Wars is full of examples of non-combat characters influencing combat. Look at R2. He’s always opening doors, throwing up smoke screens, etc.
I’m also a staunch believer that combat is a last resort in Star Wars. The empire always has more stormtroopers, so you better have a better plan than “stand and fight”. A nebulon-B frigate has 70 troopers at its disposal, and I will make you fight them all if you decide to make a stand rather than run.

A communications blackout can only mean one thing...

A communications blackout can only mean one thing...

A communications blackout can only mean one thing...

To be fair, we know hardly anything about the details of this series. 
If I were to sum up Rebels, I would say that it's about a Jedi survivor and his Padawan learning the deeper mysteries of the Force, and the role they played in the early Galactic Civil War. From what we've been told, Resistance is more about Starfighter pilots. I expect we'll see more of a "band of brothers" military vibe, than the family feel of the Ghost crew.
It would be like saying Dunkirk is a "recycling" of Inglourious Basterds just because they both take place during World War II. 

To be fair, we know hardly anything about the details of this series. 
If I were to sum up Rebels, I would say that it's about a Jedi survivor and his Padawan learning the deeper mysteries of the Force, and the role they played in the early Galactic Civil War. From what we've been told, Resistance is more about Starfighter pilots. I expect we'll see more of a "band of brothers" military vibe, than the family feel of the Ghost crew.
It would be like saying Dunkirk is a "recycling" of Inglourious Basterds just because they both take place during World War II. 

To be fair, we know hardly anything about the details of this series. 
If I were to sum up Rebels, I would say that it's about a Jedi survivor and his Padawan learning the deeper mysteries of the Force, and the role they played in the early Galactic Civil War. From what we've been told, Resistance is more about Starfighter pilots. I expect we'll see more of a "band of brothers" military vibe, than the family feel of the Ghost crew.
It would be like saying Dunkirk is a "recycling" of Inglourious Basterds just because they both take place during World War II. 

To be fair, we know hardly anything about the details of this series. 
If I were to sum up Rebels, I would say that it's about a Jedi survivor and his Padawan learning the deeper mysteries of the Force, and the role they played in the early Galactic Civil War. From what we've been told, Resistance is more about Starfighter pilots. I expect we'll see more of a "band of brothers" military vibe, than the family feel of the Ghost crew.
It would be like saying Dunkirk is a "recycling" of Inglourious Basterds just because they both take place during World War II. 

I’m on board. The combo of anime-inspired visual styles and a focus on starfighter pilots gets the wheels turning on my head.
I suspect Gundam might be a good analogue, though probably not quite as grim in tone. Gundam is animated, but there’s still an emphasis on realism. Everything feels like it operates accordig to blueprints, characters may ham it up a but but won’t take absurb pratfalls or jump 20 feet in the air if you startle them, etc.
And, ****, I’d definitely watch a show like that. Actually...
 
 
Now, I’d probably go with a slightly brighter, cleaner art style, but I think this drives home the idea that “anime-influenced” can fit pretty comfortably within Star Wars without feeling out of place.
 

I’m on board. The combo of anime-inspired visual styles and a focus on starfighter pilots gets the wheels turning on my head.
I suspect Gundam might be a good analogue, though probably not quite as grim in tone. Gundam is animated, but there’s still an emphasis on realism. Everything feels like it operates accordig to blueprints, characters may ham it up a but but won’t take absurb pratfalls or jump 20 feet in the air if you startle them, etc.
And, ****, I’d definitely watch a show like that. Actually...
 
 
Now, I’d probably go with a slightly brighter, cleaner art style, but I think this drives home the idea that “anime-influenced” can fit pretty comfortably within Star Wars without feeling out of place.