When Neeyutnee demands that Padmé inform the Senate of the possible invasion, Amidala instantly answers that they will need more proof. She is clearly remembering the events of Episode I, when a huge invasion of the planet only managed to prompt the motion of an independent fact-finding commission be sent to Naboo to ascertain the truth.

The original script had the evidence of plague be at the very start of the episode, moving downstream and affecting an entire Gungan village. Some remnants of this order of events remain in the finished episode. Notably, the tense relationship with the Gungans that Padmé cites stems from this version of the story.

The script originally called for the tactical droid to be a tripedal medical droid. This is why C-3PO says to it, "We all want to hear your tale of medical heroics."

The laboratory may have been built over a decade ago during the original Naboo invasion.

According to the script, the clones units dispatched to help invade the laboratory are Wildfire, Snow Wolves and Calm Tree.

Originally the "rabbit droid" took the bomb and left in Act II never to be seen again. Padmé found the missing bomb in the greenhouse room, left hidden for no apparent reason. The addition of the scampering droid with the bomb was done during editorial, not only for story logic but to add the fun beat where it startles Padmé.

The Naboo guards were a late addition, taxing the asset allocation budget for the episode. Consequently, the crew only produced a single guard, who was cheated in camera angles to keep the twin guards from being too noticeable.

In recreating the Theed hangar, the crew discovered that the Naboo starfighter's tails go through the hangar walls in order to fit into their stalls. Dave Filoni consulted with Episode I Visual Effects Supervisor John Knoll about this, and Knoll confirmed they had the same problem in The Phantom Menace.

In the script, the plants in the greenhouse room where Padmé finds the missing bomb were originally "tea leaf plants". In the end, Giancarlo Volpi and Dave Filoni decided it was better if the plants seemed more like they were involved in the creation of the Blue Shadow Virus somehow, hence their blue color.

The crew nicknamed the underground laboratory hallway fights the "disco hallways." Their tube-like design was inspired by the hallway Luke Skywalker explores in Cloud City in The Empire Strikes Back.