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(written from a Production point of view)
The script of Star Trek: Insurrection did not give any description of Ru'afo's flagship, leaving Illustrator John Eaves to his own devices to come up with a design for the ship, a design ethic that suited him just fine. (Star Trek: The Magazine Volume 1, Issue 3, p. 20)
John Eaves based the look of Ru'afo's flagship on two main points of visual inspiration. He stated, "I tried to combine the horseshoe shape with the inside of a piano. You see all the wires, which I thought was kind of cool." (The Secrets of Star Trek: Insurrection, p. 88) Though Eaves intended for the grand piano motif to be reflected throughout each of the Son'a vessels, he meant for Ru'afo's flagship to be a particularly strong example of this idea. "You see a lot of repetitive strings, a lot of repetitive kind of wiring going through the main architecture. And the thing with Ru'afo's ship, you'll see that through the interior of the ship." ("The Art of Insurrection", Star Trek: Insurrection (Special Edition) DVD)
As the first Son'a ship to make an appearance in the movie, Ru'afo's ship was the first one Eaves addressed. It was made smaller than the USS Enterprise-E and Eaves later remarked that it was "maybe about the same size as the dish of the Enterprise." ("The Art of Insurrection", Star Trek: Insurrection (Special Edition) DVD) The scale of the ship stayed fairly consistent. 
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In February 1998, Eaves finished up his design work on Ru'afo's ship. "I drew it to fly with the forks forward, because it looked more aggressive," he recalled. (The Secrets of Star Trek: Insurrection, p. 87) However, upon turning it over for appraisal, Eaves soon found out that his designs had been misinterpreted. "We had a lot of trouble with Ru'afo's ship [....] When I turned it over to the meeting, they had the impression that it was flying the other way. I guess I made the assumption that I always draw things flying forward and I forgot to indicate that on the drawing." (Star Trek: The Magazine Volume 1, Issue 3, p. 21)
As it turned out, it was Co-Producer Peter Lauritson who had different ideas. "There was also a funny thing, because Peter Lauritson was our effects supervisor, and when I sent the drawings over, he liked what he saw, he started getting it all approved. And then when we started to do the plan view, he goes, 'Okay, put the engines on this side, make them glow over here,' and I go, 'Oh, that's the front of the ship.' And so we had this huge kind of a discussion on which way the ship was going to fly at that point. And I had drawn everything with that kind of forward fork motion, kind of carried the architecture through it, and Peter liked the opposite view. And so I remember we went all over that drawing to make it go the right direction, carry the right way, and that was kind of funny." ("The Art of Insurrection", Star Trek: Insurrection (Special Edition) DVD)
Multiple meetings concerning the design of the Son'a flagship were held. Eaves remembered, "They did all their meetings and plans with it flying the other way, so when I got into the detailed identification of the parts, they said, 'What's the bridge doing in the back?' They understood my point of view, but it was a pretty heavy discussion on which way it was going to fly, and I fought for it pointing the more aggressive way. If you don't know you couldn't tell, but I still feel that it's going backwards!" (Star Trek: The Magazine Volume 1, Issue 3, p. 21) The discussions to and fro took almost two months, and it was not until April that Eaves presented his final redrawn design sketches with the adjusted flight direction. Years later, Eaves conceded, "Overall it didn’t really make a big difference. That is being that that was over 10 years ago, so my sadness has faded." 
Because Santa Barbara Studios was made responsible for creating all the space-bound visuals for Insurrection, the construction of Ru'afo's ship fell to that company, which represented the vessel as a CGI effect. The task was not perceived as a simple one, as SBS' Effects Supervisor John Grower remembered, "John sent us elevation views and one or two ¾ perspective drawings of each ship, but we had to do a lot of deduction work. The Son'a Flagship and Battleships had very complex shapes and all of these incredible compound curves, which didn't appear in the plan views. They're thin in one dimension and very wide and long in the other, kind of like a trilobite. The biggest challenge was that the Son'a ships didn't look the same from one angle to the next, so if we rotated around them a little bit, their profile changed because they had hundreds of compound curves that hooked together to form their shape. Getting it all to flow involved a ton of work and a very long modeling process." The model, like the other Son'a ships, was constructed in Maya software. (American Cinematographer, January 1999, pp. 41-42)