So some where in the 60+ pages of comments this may be answered..
Saw this mod, thought it looked neato! Download..install..boot up..
Uhm; where do I encounter the new ships? Do I need to start an entirely new game for that to work, or will my current one work? I'm curious is all. I had one random Legion encounter <I think it said Legion> but it was just standard low tier pirate hulls that quickly died to my swarm of autocannon equipped ships and I saw nothing in loot that was new..
... First off, have you got any other mods installed?
If the answer is "None" then that's your problem: SCY requires a couple of under-the-hood "library" mods ("LazyLib" and "TwigLib") to operate it's advanced game features, and if you don't have them it won't actually run.
What's confusing me is what this "Legion" encounter of yours is. :/ Wat? I presume it's from another mod, which contradicts my first thought, but I can't think what. There's certainly no "Legion" in the stock game.
Also, regardless of what mods you've installed, you will almost certainly need a new world/save to introduce the relevant faction/ships/stations/systems etc.