Through the fic, Team Rocket performs two major genetics projects. One of them is the sekritlike Tribo, the other is the world-changing Orthan. Orthan is an anagram (click here to see what of), and a clever one too. The project itself entailed years of research into Pokémon genetics, and months upon months of preparation for only several hundred test subjects.
Orthan itself transforms almost any Pokémon into, basically, human-shaped creatures who look like someone's dressing like a Pokémon. What good is this? Well, I'll tell ya. It increases their strength and intelligence severalfold. Orthan Pokémon are, well, faster-stronger-better than most normal Pokémon.
Team Rocket didn't consider the psychological implications of such a horrendous transformation, however. It wasn't out of cruelty, it was out of a strange combination of detachment and lack of consideration for the Pokémon. It would be unfair to say that the repercussions weren't unforseen, although they certainly didn't stop the Project from going forth. Many Orthan Pokémon become depressed, a few suicidally so, and are viewed as freaks of nature. A lot of trainers who had their Pokémon stolen and experimented on don't want to associate with their former Pokémon. Other times, a lot of Orthan Pokémon don't want to be with their former trainers again. Former wild Pokémon feel out of place in the wild again. Very few Orthan Pokémon can cope well with their changes and at the same time have former trainers who will support them (Alex accepting a mostly-faring-well Marril is an uncommon reaction).
That isn't to say that Orthan Pokémon are universally despised. They aren't. In general, however, the change was so radical and yet only an annoyingly large small amount (seven hundred and something) were modified before a security breach shut down the project, so Orthan Pokémon are not only considered freaks, but they're also very rare. The Pokémon League, as the government on anything Pokémon-related, has a tough time deciding what an Orthan Pokémon's rights should be.
Other random things about Orthan Pokémon include the fact that pokéballs don't work on them, that they can't evolve by any means, and that despite the fact that they were once Pokémon, the average Orthan Pokémon doesn't very much like fighting.
On the whole, Pokémon SS doesn't delve very deeply into all of this, although glimpses it offers of the aftereffects on the world are common. Orthan Pokémon aren't even that well-known, however, since there are less than a thousand between all of Kanto, Johto, Hoenn, Orre, and Idama (a nonsensical Japanese-sounding word that I made up for the country the Neo League is in). Most people have never seen an Orthan Pokémon, let alone met and talked with one, as such since Alex and Tschel move about in the world most people assume Marril is simply a human who dresses like a Pokémon.
It's an anagram of "anthro", short for the word "anthropomorphic", or human-shaped.