Red Mage timeline

Something is bothering me and I need profssional help (Moose, Koji, Yoshi...etc).

It's about the red mage story, so if you haven't done it, don't read the rest.

And start leveling a red mage because it is even better than ninja.

So the red mage story, much like the job itlself, is several kinds of awesome. It features mentions of Alisaie, a cameo from Riol and a trip to the Gold Saucer. Plus a few GoT nods.

However there is one weird part. We go and invade Castrum Meridianum and fight a quite larg imperial patrol.
Why is that a problem? Well, during the finalee of 2.0 Castrum Meridianum gets invaded and large chunks of it get blown up. At least twice. And this is a level 58 quest. During which X'rhun tells us it was Crown Prince Zenos who came up with the bad guy's plan. But he didn't become crown prince till Varis ascened the throne during 2.5 if I'm remembering correctly. X'rhun also aknowledges us beating Zenos if we got that far.

So why are there still Imperials in CM? Is what's left of it not under Alliance control?

From what I remember, during Operation Archon it was never the Alliance's intention to completely capture the castri in Eorzea, but merely surround and blockade them (basically besiege them and cut them off from each other), as the Alliance simply did not have the manpower to capture the entire legion whole. Instead the Alliance wanted to prevent them from reinforcing CM while the player and their 'elite adventurer unit' infiltrated the Praetorium to destroy the Ultima Weapon (the real objective of Operation Archon).

Even though the Praetorium was reduced to a smouldering ruin by Lahabrea casting Ultima, CM was still intact, and after the destruction of the Ultima Weapon and Gaius's death, what's left of the XIVth remain holed up in there and the other Castri - this is why you still see Garlean troops in those castri after 2.0's story is completed, they're remnant forces (although Castrum Oriens is eventually cleared of remnant Garlean troops during Baelsar's Wall's story, which the Alliance then occupies afterwards, forming the entrance into Gyr Abania in SB). Raubahn actually stated this in the 2.0 ending scene in Mor Dhona following Operation Archon, "that although the Black Wolf is slain, the rest of the pack remains" (paraphrased).

Either way, the Garlean castri in Eorzea still have remnant troops within as the Alliance simply does not have the resources to clear those facilities out, so they just blockaded them instead.

I've yet to do these quests so I needed to do a bit of research, but I think Enkidoh has hit upon the point that will be of the most use to you. As far as the XIVth Legion knows, their status as rogues who removed themselves from the chain of command means that no help is coming. Nero says that execution awaits him in Garlemald, but he was a leader of the legion - who knows if they'd subject rank-and-file to the same punishment (since they would have to be insubordinate to every other link in the chain of command to obey then-High Legatus Varis; unrealistic at best, more likely ill-advised in general). At the very least, no evacuation is coming (because those NPCs are open-world and can't really go anywhere...)

After Baelsar is (allegedly) slain, the XIVth - leaderless and abandoned - retreat into the castrums and fortify them. Since then they've been reduced to scavengers and outlaws, but if they haven't tossed aside their uniforms or surrendered themselves to the Alliance, at least some must have some loyalty to Garlemald. Zenos involving them in his putting Lambard to use likely just seemed plausible enough to wedge into a job scenario.

Ah, okay. A lot of time for stragglers to be around but makes sense I guess. I figured the answer is something like this, but I had to be sure.

I haven't finished the story yet, but I recommend doing it Moose. It is fantastic.