S-CRY-ed/WMG

Kazuma and Ryuhou are alters of Kanami.
Both Kazuma and Ryuhou have vague origins; Kazuma doesn't even have a full name. Also, Kanami is always dreaming about both of them. Finally, at the end, when the two fight, they both die. In the epilogue, Kanami is shown using her alter, and then Kazuma and Ryuhou are back: she resummoned them. Most likely, they were initially summoned subconsciously.
 * Possible with Kazuma, not with Ryuhou. He's seen as a child, and grew up with a rich family.
 * Where do you get that they die? Right at the end of the fight, one of them (probably Kazuma) raises his hand and makes a fist, so at least one of them survived that fight.
 * He/they may have succumbed to his/their injuries.

Kazuma and Ryuho end the series as a merged being.
Kazuma and Ryuho both survived that final battle... as a merged being (a bit like the outcome between Dragonlance's Raistlin and Fistandantilus). Note the semi-vague character of the hand gesture at the end: it starts like Ryuho's knife hand, but then changes to a fist. They're both there.

Alters are derived from Forerunner technology
The Lost Ground was formed due to seismic activity sometime in the early 21st century. Who's to say that wasn't caused by some ancient, unseen Forerunner Artifact of similar design to the one in Kenya. Although the Human-Covenant War probably occurred over 5 centuries after the events in Scryed, the similarities are there:


 * It is possible that alter users do not break down and reform matter as it appears, rather they transmit/materialize matter via slipspace. The "Other Side" which many characters in the show speak of may be either an alternate, slipspace-only dimension where matter is constantly reforming and shaping itself as alter parallels to beings in the physical world, or it may be some sort of Forerunner installation designed to study/contain the slipspace technology which is required to form the alters. Notice also that the series never (from what I've seen) mentions people using alters anywhere in the world other than the Lost Ground and the Mainland. Perhaps the transmutation effect is lost when one moves outside of the unseen artifact's effective radius?


 * This may be cancelled out by the fact that we see alter users break down matter from the surrounding environment to make their alter. However, that might be the effect of whatever Applied Phlebotinum is required to transmute matter out of slipspace, possibly creating antiparticles that are what's actually appearing to disintegrate matter. The fact that sometimes the matter returns to whence it came and reforms the disintegrated item(s) may support the slipspace hypothesis. What if the matter from the item is required to be transferred into slipspace, swapped for the alter-making matter, then switched back again when the alter is no longer needed? The theory is similar to a computer's memory buffer - there are two regions, and only one is visible. The invisible one temporarily holds something (data, or in this case matter) while the visible one actually uses/displays it.


 * Alternately, perhaps alter users do reform and transmute matter without using slipspace. We haven't seen a bunch alter-like technology in the Halo games themselves, but what we have seen seems, to me, rather similar to alter technology. Take the so-called "light bridges," for instance. There's no way photons can be made hard in real or near-real physics, so there must be some form of unseen field which shapes minute particles of matter into a crystalline form such as a bridge, which when held together by the unseen "alter field" provides a structure strong enough to drive a Warthog over. Additionally, this crystalline matter could be made to explode or be used as a weapon, as in the Covenant needler. I remember the UNSC not knowing a damn thing about how needlers work, so one possible hypothesis is the needler is a type of mass-produced alter that keeps its form rather than breaks apart when not needed.


 * The same could be said about many other Covenant and Forerunner technologies. From a less sophisticated standpoint I'd say a lot of Covenant technology (also Forerunner, but especially Covenant) resembles many of the alters we've seen in s-CRY-ed, especially the "refined" ones used by HOLY. This is interesting considering most "native" alters seem slightly more angular and crude-looking, often being shades of red or gold (as in Kazuma's alter, which is not angular or crude-looking at all) while most used by HOLD/HOLY seem slightly sleeker or curved, and are almost exclusively shades of blue, green, purple and white. The result looks very similar to Covenant technology, so I can assume that perhaps the Covenant use the same sort of "refinement" process for their alters that HOLD does.


 * Jiralhanae (Brute) weapons tend to look strikingly similar to native alter technology, as opposed to HOLY technology. But because they are the most primitive race in the Covenant, and seem to lack Forerunner technological influence, it's doubtful their technology is alter-based. Additionally, UNSC A Is like Cortana take on a somewhat alter-like appearance, but it's doubtful that they themselves are alters, or that the UNSC has any alters of their own, though it's hard to confirm this.


 * One final word in favor of this hypothesis is the fact that the UNSC haven't even begun to understand Covenant weapons technology, since you cannot recharge/reload Covenant directed-energy weapons, and any Covenant projectile-based weapons must be replenished with Covenant ammuniton only, as the UNSC cannot build their own analogues to Covenant projectiles.

Scryed takes place several years before Needless.

 * Face it, there's little difference between Alter Users and Needless.
 * THE LOST GROUND IS THE BLACK SPOT !!!

Alters run off of Spiral Power.
Alter users have the ability to reconstruct matter (while spiral power creates matter, no one ever said they had perfected using it) into weapons for them to use. Kazuma is Hot Blooded and one of the strongest ones, and Ryuhou gains more power when he becomes Hot Blooded. Oh, and Kazuma sounds like Kamina.

The entire series was All Just a Dream
Kanami's dream. Kanami practically says so herself throughout the series, as well as the show's name. If she were seeing real events, it's doubtful she never recognized "the man in my dream". She only refers to Kazuma and Ryuhou by name when she's talking inside the dream; never in her narration. The disaster, Lost Ground, Alter users, etc. may or may not have actually happened. If they did; Kanami's narration is her describing her dreams to a (possibly HOLY) specialist, perhaps still unsure whether she has an Alter or is just having a bizarre series of extremely vivid dreams. If those things didn't happen; it would be relatively unchanged, just without her Alter or HOLY, and with the dreams being more bizarre.