Manga Summary
Broadly speaking, the manga version of s-CRY-ed (which technically came before the anime) plays out against the same background as the anime - we have a Lost Ground, a bunch of Alter Users running around, the Inners vs. HOLY thing, and so on. It's in the actual series progression that it deviates from the more popular anime.
We start off following an Alter User by the name of Kazuma Torisuna (yes, this is the same Kazuma, but he has a last name - it literally translates to "treasoner," which we see him referred to as frequently) and his mercenary explaoits across the Lost Ground. Eventually, while on a job, he runs across Ryuhou, they generall hate each other, and so forth. Along the way, Kazuma gets picked up by an anti-HOLY organization known as LAWLESS, HOLY bases are raided, general Alter-on-Alter mayhem, the appearance of an elite HOLY organization known as Super-HOLY, and finally a massive confrontation with Martin Zigmar (there's no "L" at the end of his name in the manga translation)... who is a far different individual from the Zigmarl of the series.
It should also be noted that the s-CRY-ed manga is quite a bit more graphic than other adaptations of the series. There's plenty of blood, gore, and quite excessive nudity. The U.S. release by TOKYOPOP was rated OT (16+), but it could just as easily warrant a Mature rating. In short, it is pretty much a soft porn manga - and not for the soft of heart. Some of the same political undertones seen in the anime are in the manga, but they're more subdued, and somewhat overwhelmed by the combat and blood and excessive panty-shots.
Overall, the anime is generally preferred by fans, but anyone interested in getting the whole picture of the s-CRY-ed fandom might want to check out the manga.