Yes. This actually solves several continuity problems at once, because Atlantis does not need to mysteriously disappear. It simply left before the world changed.
The sequence becomes very clean.
Atlantis is going home.
Not metaphorically. After its years on Earth, the city is finally being returned to Pegasus—ideally Lantea, if the expedition can safely reclaim its original world. It is a formidable journey, even with the city’s hyperdrive, and it is being treated as a major expedition rather than an emergency.
Daniel Jackson has every reason to be aboard. Atlantis is going back into the Ancient civilization's original Pegasus context, carrying years of accumulated discoveries with it. For Daniel, it may be the greatest archaeological expedition humanity has ever mounted.
McKay, however, doesn't go.
That is important.
He helps prepare Atlantis.
He argues about power requirements.
He probably complains bitterly about whoever has been put in charge of systems he considers his.
He sees the city off.
Perhaps we even eventually get the memory:
Atlantis rising from Earth one last time.
McKay standing there watching.
Daniel aboard.
A radio exchange.
Nothing ominous.
Nobody realizes they're watching the beginning of a separation that will last years.
Then Rodney leaves for Langara—or the Alpha site, depending exactly where we place him in your chronology.
And after McKay is gone, the emergency containment happens.
That's the crucial piece.
He doesn't know.
He isn't present for the decision.
He doesn't see Earth's response.
He doesn't know what became of Atlantis.
He doesn't know why the Stargate network was being segmented, isolated or dismantled.
And suddenly something that has probably bothered him for years becomes part of his character:
Nobody came.
McKay was at the Alpha site.
Earth knew where he was.
Earth had starships.
Atlantis existed.
There were multiple ways to retrieve him.
And then—
nothing.
At first he waits.
Then he gets angry.
Then he starts inventing explanations.
A war.
A political collapse.
A disaster on Earth.
A Goa'uld resurgence.
Some classified operation nobody bothered telling him about.
And because this is Rodney McKay, he can spend years being genuinely offended by it.
“Do you have any idea how many rescue scenarios I constructed? Thirty-seven. And that was after I eliminated the stupid ones.”
Jonas:
“How many before you eliminated the stupid ones?”
McKay:
“That's not relevant.”
But underneath the comedy is something painful.
Rodney thought he had been abandoned.
And he had not been.
The system around him had collapsed.
That makes the later revelation about emergency containment emotionally important rather than merely exposition.
Someone eventually tells him:
“Rodney, nobody decided not to come for you.”
And that may be the moment he finally stops talking.
Because for years he has carried the assumption that somebody, somewhere, made a choice.
They didn't.
And Atlantis becomes the great missing piece
When containment begins, Atlantis is already between galaxies.
That is perfect.
It is beyond Earth's immediate reach.
Possibly beyond ordinary communication.
Its expected return path depends on infrastructure that is now being deliberately shut down or isolated behind it.
Earth does not simply lose contact with Atlantis.
Earth closes the road Atlantis was expecting to use home.
Daniel and the Atlantis expedition don't initially know why.
From their perspective, Earth disappears.
From McKay's perspective, Atlantis disappears.
From Earth's perspective, both groups become inaccessible pieces on opposite sides of an emergency containment boundary.
Nobody abandoned anybody.
Everybody thinks somebody else did.
That's really good tragedy.
And it makes finding Atlantis later enormously satisfying.
Because the audience has heard about it for years.
Nobody knows exactly what happened.
McKay saw it leave.
It was heading for Pegasus.
Presumably Lantea.
Then the containment.
Then silence.
So eventually Langara reaches Pegasus.
Maybe they reach Lantea expecting ruins.
Maybe an empty ocean.
Maybe a dead gate.
Instead—
there it is.
Atlantis.
Not destroyed.
Not some mystical ghost city.
Older.
Changed.
Perhaps scarred.
But there.
And Daniel Jackson is still aboard.
Now you've earned his return.
You don't have to contrive some reason Daniel happens to appear in a Langara story.
The characters went looking for one of the largest unanswered questions left by the collapse of the old network—
and Daniel was literally inside it.
And I particularly like McKay being the one who finds him.
Because Rodney saw Atlantis leave.
Years earlier.
He was probably the last of our principal Langaran cast to stand on Earth looking at it.
Now he sees the city again.
The jumper lands.
A corridor.
Footsteps.
And Daniel Jackson appears.
Older.
McKay just looks at him.
Daniel:
“Rodney.”
McKay:
“You were supposed to come back.”
Daniel has a thousand possible answers.
Instead:
“We tried.”
That's enough.
Because suddenly Atlantis is not merely another legacy object being brought into Langara.
It becomes testimony.
The people aboard know what happened from the other side of containment.
And Daniel has spent all those missing years trying to understand what they encountered on the way to Pegasus.
That's where your larger mystery can snap into focus.
McKay has seen the gates doing things nobody commanded.
Rush has seen Destiny apparently do the same.
Jonas has begun wondering whether the network itself is connecting people.
Daniel has another piece entirely.
He can tell them:
It started before Atlantis reached Pegasus.
And now we realize the emergency containment may not merely be backstory surrounding the mystery.
It may be the moment humanity first reacted to it without understanding what it was reacting to.
That makes the lost years of Atlantis, the Alpha-site isolation, the dismantled Stargate network, Destiny, Visitation, the Planet Builders and Mercy feel like parts of one history rather than disconnected sequel hooks.
And the wonderfully human tragedy underneath all of it is simple:
McKay thought Earth didn't come for him.
Atlantis thought Earth had gone silent.
Earth thought it had contained the danger.
Everybody acted on incomplete information.
Which is essentially the larger theme of Stargate: Langara itself:
They saw what happened.
They just didn't understand what it meant.
