Dr. Mora (James Sloyan), the scientist who helped Odo develop his shapeshifting abilities, and also a father-like figure to the rogue Changeling, comes to DS9 to reconnect old bonds which have grown apart since Odo left Bajor in search of something better than being a "science project." Meanwhile, an Unknown Lifeform [TM] that Mora and Odo have brought back from the Gamma Quadrant (which, by the way, may be a clue to Odo's mysterious origins—or not) roams the station and attacks people, in a plot akin to a B monster movie.
If ever there were an episode with a split personality, "The Alternate" is it. There are two ideas here that the writers must've been set on jamming together into one, never mind that they really shouldn't have had the slightest reason for coexisting. Nevertheless, "The Alternate" manages to be a riveting show on some levels, even if it's the epitome of mediocrity on others. The Odo/Mora scenes are fantastic, opening the backstory to how Odo became who and what he is, even how his personality came to be. Sloyan is superb as Dr. Mora, and Auberjonois' turn as Odo is a highlight that exhibits attitudes that are far more "personal" than the character typically takes on.
Then there's the lifeform plot, which is filled with long stretches of dull scientific exposition, technobabble, bizarre red herrings, and even a few suspense scenes (some of which actually work). The episode's twist is that the lifeform is actually Odo in an uncontrollable shapeshifting state, who chases after Dr. Mora because of gas particles that have been absorbed into his (Odo's, that is) cellular structure. As implausible as it probably is in plot terms, this explanation somehow manages to have some moving emotional implications in the Odo/Mora storyline, driving home a bond the two realize they need to reopen and reevaluate. But couldn't this have been done without so much mundane (and unlikely) underlying subplotting?
Note: If you watch this episode again, you'll notice a blatant change in character backstory. There's a dialog scene here that strongly suggests (more like flat-out says) that Sisko's father had died years ago. Look at the scene where Sisko offers words of wisdom to an Odo concerned about Mora's condition after encountering the toxic gas: "In the end there was nothing [my father] could do, and nothing I could do." This is contrary to "Homefront," in which we learn Sisko's father is still quite alive.