Spoilers Off apply to all moment pages, so proceed with caution. You Have Been Warned. In this instance, these theories may rely upon familiarity with the game's story.
Notice how extensive the modifications to Kane's body were, looking a lot more involved than a press lowering and instantly transforming Kane. It's possible that Kane had memory blackouts of the most traumatic experiences, as suggested by the part where a circular saw removes much of his legs. It's likely there were forgotten parts where Kane was in intense agony and being operated on by Scientists, especially considering Kane's high value to the Strogg.
The Strogg had a fail-safe plan in the event that The Nexus was taken out, and Kane must now play a role in helping counter the Strogg's backup plans as well as their new leader. The Makron that Kane defeated wasn't irreplaceable either.
There was a fail-safe in the Strogg Neurocytes just in case the Nexus Core was taken out and their leadership left in disarray. The remaining Strogg were ordered to assemble at a staging point in order to regroup and organize their counter attack. With this threat, Kane will be all but forced to return to Earth and we will see how the population deals with his Stroggification and how Kane's heroism makes him into a superhero of sorts to the world. In short, it's Hell On Earth, but with Strogg instead of Demons.
When you arrive at "The Nexus" proper, the hallway is lined with ammo and supplies like the Makron wants Kane to stand a chance. This seems uncharacteristic of the Makron's personality, unless they were trying to fatally break free of their neurocyte and found a workaround by leaving ammo strewn about in the final hallway (justifying it as supplies for his Tactical Strogg teams). Scott Voss was able to hold off the influence of his neucrocyte temporarily so it's possible the Makron had learned ways to work around his implants partially. Maybe they also wanted Kane to destroy the Nexus to dismantle the Strogg network and make it easier to free the enslaved species.
There was a cut mission pack called Awakening in the works, which ended up being scrapped after IV failed to meet sales. Some guesses as to what the possible plotlines could have been:
- Much in the same way Doom Eternal and The Ancient Gods 1 & 2 revealed the origin of the demons in the Doomverse, Awakening would have the origin of the Strogg as a main plot point.
- A Boss fight against a rebuilt Makron... as a Mid-Boss. The Final Boss would either be a HAL9000/Skynet Expy or worse: a cyborgized human with God-deliriums.
- Much in the same way the Hornet went from a Mid-Boss in II to a Degraded Boss in IV, the Network Guardian would be degraded from a dragon to a more present enemy.
- A bit of Gameplay and Story Integration regarding the way the enemies vanish after being destroyed: turns out there's a Nexus-esque device/structure that must be taken down so all Strogg deaths are final. The consequence, of course, is that this would also affect Kane.
- For plotline reasons, several areas of II and IV would be revisited, such as Outer Base/Installation (with Dark Reprises of "Descent into Cerberon" and "Quad Machine" as part of the OST), the Strogg Medical Facilities (with a possible mission to shut down permanently the whole facility).
- The Makron has weaponry that could be derived from the Black Widow's arsenal such as the dark matter weapons being derived from the disruptor &/or anti-matter technologies. The beams the Makron fires are a spin on the Plasma Beam. In other words, while the ending of Quake II: Ground Zero isn't cannon — Strogos wasn't obliterated by an anti-matter bomb naturally — the technologies shown in Ground Zero live on such as the Dark Matter, Nailgun, and Lightning Gun (an offshot of the Plasma Beam) technologies.
- Having both been captured and experimented with by the Strogg, they'll both be able to relate to each other. It's a potentially cool concept and an opportunity to give Kane a voice actor along with Bitterman.
For Example:
- The Quake II Hyperblaster is a different design that the Strogg replicated from the model we see in Quake IV, hence the reason it has Bottom Less Magazines and looks rusty and dingy. This model never made it into widespread product before the Big Gun was destroyed and the original Makron was assassinated so the Tactical Strogg used the captured models that have limits like the limited magazine size. However, these models would be presumably be lighter due to the smaller batteries rather than whatever power cell the QII Hyperblaster used. Bitterman — Stroggified himself — wouldn't have trouble wielding a Hyperblaster's presumably high mass due to its 300-shot-cap onboard power cell.
- The Quake II shotguns are presumably both drum-fed, explaining how the game shows them never needed a reload. They do require reloading, but for gameplay reasons, it's not a mechanic.
- The Chaingun is an experimental portable Strogg Minigun, not usually carried by marines in story due to its still considerable weight. Bitterman, being stroggified himself can easily handle it. The Chaingun uses the relatively low-caliber Machine Gun bullets to help lower weight. The Nailgun was an off-shoot of this concept, having much better portability (Kane can carry it before his Stroggification!), and the optional homing feature to compensate for the slower nails.
- The BFG10K was derived from blueprints the Strogg obtained for the original BFG 9000! The first Makron took a liking to this weapon, hence why they wield it even though the Painfully Slow Projectile gives it dubious utility against the agile Bitterman. Good intimidation weapon perhaps. And considering that the Doom and Quake series have crossed over twice, this isn't as far-fetched as people think it is.
