Droid Control Ships
For years, consumers of the galaxy have lived with the familiar massive sihouettes of Trade Federation cargo vessels orbiting their worlds and plying the spacelanes. Now these huge behemoths house more than just goods for sale or trade...many of them have been converted into warships and Droid Control Ships, and an unsuspecting galaxy can't tell the difference.
I refer you, once again, to Star Wars: Episode I Incredible Cross-Sections...
"From the very first stages of planning to build their secret army, the Trade Federation armaments committee had in mind the use of their great commercial fleet of giant cargo ships for transporting the weapons of war. Familiar to millions of officials and civilian personnel who dealt with them over the skies of numerous planets, the characteristic giant Trade Federation cargo ships had been built over many years, plying cargo among the far-flung stars of the galaxy as part of the extensive market of the Trade Federation. These seemingly harmless and slow-moving container ships would now hide, deep within their hangars, the tremendous army built to change the rules of commerce. Upon the first complete council approval of the secret army plan, the cargo fleet was brought under study, and by the end of the project's construction phase the Neimoidians had created from them a frightening fleet of warships.
War Conversions
The converted battleships bear unusual equipment for cargo freighters, including powerful quadlaser batteries designed to destroy opposition fighters launched against the secret army transports. These batteries are built to rotate inward while not in use, concealing [the vessel's] true nature until the Neimoidians wish to uncloak their military intentions to unsuspecting 'future customers.' While the cargo hangars and their ceiling racks in the ineer hangar zones proved sufficient for the carriage of the secret army ground forces, additional large electrified racks were installed in the outermost hangar zones to quarter the dangerous colonies of droid starfighters, which draw power from the racks until launch.
Civilian Compromises
While the Trade Federation cargo fleet was ideal for hiding the existence of the secret army and carryingit unobtrusively to points of deployment, the commercial origins of the battleships leave them with shortcomings as 'battleships.' Fitted with numerous guns around the equatorial bands, the battleships carry considerable firepower with very limited coverage and so large areas of the ship are undefended by emplaced artillery. The onboard swarms of droid starfighters are thus essential for defense of the battleships from fighter attack.
The Hand Behind the Secret Army
While the Trade Federation has long been known as a greedy and conniving organization of merchants, the use of armed force to increase their profits hardly seems to suit their fairly cowardly nature. A strange force has been at work within the Trade Federation, making it capable of extraordinary measures and committing it to a course of conflict and outright war that will shake the very Galactic Republic. At its core, the Trade Federation's secret army appears to be the vision of a shadowy figure called Darth Sidious, who has been manipulating powerful Neimoidians to do his mysterious bidding. The Sith title of this dark lord holds menace for all, and no one can guess where this disturbing course of events will lead.
Droid Control Ship
The single critically important vessel among the Trade federation fleet of battleships is the Droid Control Ship. Custom-fitted with massive transmitters, receiver antennas, monitor sensors, and numerous additional reactors and power substations to run them, the Droid Control Ship contains tremendous computer banks and the Control Brain Network, which transmits the signals vital to the functioning of every battle droid in the Trade Federation army. From this one Droid Control Ship is broadcast the control signals that direct each droid's actions, making up for the very limited onboard logic systems of the minimalist droids. Without this constant signal and its stabilizing carrier wave, the battle droids would be useless 'terminals,' incapable of independent action or self-control."
According to The Essential Guide to Droids by Daniel Wallace, Bill Hughes, and Troy Vigil, robotic infantry soldiers have never been largely successful in the Star Wars universe, even in the years before the Republic. Some groups had limited success with particularly good battle droid concepts, such as the war droids of the Krath and the Mandalorian Basilisks (from the Tales of the Jedi comic books from Dark Horse Comics), but in the "modern" era, such concepts have been largely eliminated by advanced signal jammer technology and so forth. (These earlier droids were used more as commando units anyway, and had more complex "independence" programming, being designed to operate in smaller numbers). I was curious about this detail when I first viewed Episode I...if the Neimoidians can block Naboo's communications, thus proving that signal-jamming technology does exist in this era, couldn't a people under Trade Federation attack simply use a signal jammer array to shut the invading droid army down? The Naboo know that the signal guiding the droid army comes from an orbiting Control ship, so it's not as if the fact that a remote signal is being used by the Federation is a great secret (they've had these droids for years, just never in such large numbers). I can make only three guesses as to why this didn't happen:
1. It's possible that since the Naboo had no idea that a large army was orbiting overhead, their peace-loving government hadn't made provisions to put large jammer arrays into use; or...
2. the technology for signal-jamming isn't advanced enough in the Prequel-Era to do the job (as readers of the Star Wars books know, communicating in space without using the Galactic Holonet can be screwed up by a great many things, making the blocking of communications relatively easy, but the droid signal is stated as having a "carrier wave" by the quoted text above, so it's possible that the carrier wave prevents this era's jammers from working on the signal); or...
3. it's been so long since anyone tried deploying a droid army (the Tales of the Jedi comics are set about 4000 years before Episode I) that nobody has signal jammers of a scale big enough to deal with the droid army in this fashion any longer, and many planets may not have even developed them yet.
Well, there had to be a technical question or two raised by telling a prequel story in such a technology-laden galaxy, in regards to what exists in the Prequel-Era and what gets invented between Episode I and Episode IV...
GMs will more than likely be called upon to make a judgement call on this matter if they put their PCs up against a Trade Federation army. My advice? Dodge the issue! The only safe way out of this one is to entirely avoid the risk of being contradicted later by Lucasfilm (and hearing your players malign you for it)! More than likely, Episode II or Episode III will resolve this question (I'm betting on Anakin developing a jammer that will crack the signal in Episode II, thus setting the stage for the advent of clones being used in warfare instead of droids...the Clone Wars are supposed to be in this trilogy, you know...). Until then, amuse yourself by finding clever ways of making jamming impossible or too impractical...have the battleships protect the Control ships at distances where jamming the source is a pipe-dream (signal-jammers are narrow-focus, not broad-band)...have ground-based jammers frequent targets of Federation forces before they can ever be used (to power such long-range jammers would take a LOT of juice, and enough warm-up time to let the enemy know the apparatus was there)...stuff like that. It's only a couple of years until Episode II. Until the truth is known, give the PCs other matters to think about.