Mysteries of the Sith is an expansion pack to the second entry in the Dark Forces Saga, Jedi Knight. In some ways it improves upon its predecessor, and in some ways its a few steps back.
The game gives you a good, if false, first impression in the opening level. While Kyle Katarn is training his new apprentice (smuggler-turned-Jedi and future wife of Luke Skywalker, Mara Jade), the Republic base they're at is attacked by the Imperial Remnant, using space stations disguised as asteroids to ambush their enemy. You spend this section playing as Kyle, and its a breath of fresh air from Dark Forces II with a sprawling, semilinear level and two or three new varieties of Stormtrooper to fight.
However, this level was either designed to catch your attention so you'd be strung along with the rest of the game, or was indicative of the original vision that ultimately didn't pan out, as once you move on from the Republic base things quickly deteriorate into largely linear run-and-guns punctuated with both the unintuitively specific progression of Jedi Knight and at times the baffling moon logic of the original Dark Forces. The impressive scope of Jedi Knight is also lost, leaning more towards the relatively cramped and linear confines of the later Jedi Outcast. One notable exception to this is the final level in the Sith Catacombs, which involve a series of puzzles spread along the perimeter of a massive central chamber that gives your efforts a sense of continuity and scope.
Finally, the story is the absolute thinnest of the series, which given the flat characters and often thin establishment of Jedi Knight, says a lot. While I never was at a loss as to what I was doing at any given location and why, there is no overarching story to the game whatsover. After the initial attack by the Imperial Remnant, Kyle leaves Mara Jade behind to look into an unrelated matter, and the Imperials never come up again, apart from a minor occupying force on a later planet that never factors into the plot at all other than as someone else to shoot. Mara is left to run errands for the Republic in the meantime, first by gaining the assistance of a crimelord for supplies, then by guarding and then recovering a Jedi Holocron when it inevitably gets stolen by pirates. Absolutely none of these things relate in any way to each other or the final act, other than Mara's hand in all of them.
Mara Jade is a more interesting person than pre-Jedi Outcast Kyle Katarn (being little more than a gun-for-hire in Dark Forces and a bland grizzled action hero in Jedi Knight), but she is without question the most horrible person I've ever played in a Star Wars game who wasn't a Dark Sider trying to make their puppy-kicking quota. When sent to negotiate with the crimelord I mentioned earlier, the doorman speaks highly of her former smuggling career but says his boss is uninterested in seeing her due to distrust of the straight-laced Jedi she seems to have become. Her response? Kick down the back door, murder about 80% of the crimelord's employees, and then force him into negotiations at gunpoint. He relents in return for a favor, but the fact that we're supposed to be rooting for Mara here kind of disturbs me.
Once that's dealt with (an affair that mostly involves a chase through a city, being captured, killing a rancor, and then fighting your way out of your target's base), the crimelord agrees to a business relationship with the Republic, but not before Mara Jade decides to blackmail him one more time, just for kicks. This plotline never comes up again, as we next see Mara overseeing the transport of a Jedi Holocron, when her ship is attacked by pirates and she's forced to smuggle herself onto their ship, fight her way through their docking facility, then to the base of the collector it's been sold to in order to retrieve it. This plotline has nothing to do with anything else either.
Finally, Mara decides to go looking for Kyle as she hasn't heard from him since he took off on his private investigation. At this point the game largely plummets into Xen Syndrome, as you wander through a swamp with nonsensical puzzles (you can't pass unless you use Force Persuasion on the statue? What?), overpowered enemies that will kill you in two hits (and in the case of the trash-squid things, can't be killed at all for some reason despite Kyle gunning down a dozen or so of them in Dark Forces), and the complete inability to use any weapon except your lightsaber for the rest of the game. Oh, and there's Sith Zombies for some reason, because I guess that's a thing now.
It turns out that the strong Dark Side aura of the ruins on this planet sent Kyle, who has been established as a borderline-neutral individual throughout the games, off the deep end into crazy Sith hermit. Exactly what happened to twist him that way is probably a more interesting story than the actual game, where after a few ignored attempts to get you to either ♥♥♥♥ off or join him, he decides to finally try and kill you dead, at which point your only option is to turn off your lightsaber to convince him that he's not far gone enough to start offing his friends. At which point you leave, the credits roll, and two massive plot points that occured between this and Jedi Outcast (Kyle switching from a yellow to a blue lightsaber and eventually giving up his Force powers) are left entirely unadressed.
In summation, this game is roughly on par with Jedi Knight in quality, with every improvement balanced by a downgrade. And much like Jedi Knight, I ultimately can't recommend the experience. Basically nothing happens over the course of these two games couldn't be guessed at based on offhand comments in Jedi Outcast, and quite a few things that ARE mentioned in Jedi Outcast are never actually addressed in these games. Not needed for the story, and the gameplay isn't up to snuff with Dark Forces or Jedi Outcast, so just play those and skip these lesser installments.