We see the Helicarrier again in Age of Ultron, and get a hint of what it’s been up to.
When Nick Fury pulls up in the Helicarrier, he says “Nice, right? Pulled her out of mothballs with a couple of old friends. She’s dusty but she’ll do.”
The implication seems to be that the Helicarrier has been in storage since it was damaged in Loki’s attack, and he’s quietly had it patched up and restaffed. (Since some of the original staff are probably HYDRA and/or dead.) The “old friends” include Maria Hill and the SHIELD technician who we last saw standing up to Rumlow in Winter Soldier (I incorrectly said this was Danny Pudi; it’s actually Aaron Himelstein).
Apparently this is something we’re going to learn more about in Agents of SHIELD. In an interview with Slashfilm, Kevin Feige confirmed that we’re going to see more of this:
Now, when Nick Fury goes away and comes back with a Helicarrier, that seems like a big chunk of off screen story. Is that something we might see referenced on SHIELD?
Feige: I think it’s fair to say you could fill in some of those blanks in the coming weeks on Tuesday at 9.
Since it didn’t happen last week, maybe it happens this week. Maybe next. But according to Feige, we’ll get a storyline on the show that’ll cover where Fury goes to get the Helicarrier that he brings in to aid the Avengers in their climactic battle with Ultron.
We see the start of this storyline in Agents of SHIELD s02e20 “Scars”:
At the start of the episode, we see Coulson arriving at a new base, staffed with another of the Koenig brothers. This is what “Theta Protocol” is about: the repairs of the Helicarrier. He is shown to a hangar bay:
Note the “64” on the deck: this is the original Helicarrier. I believe the cargo in the top-right hand corner is what we see in Age of Ultron, but I’m not sure.
Later, Coulson explains to the rest of new SHIELD that this was a “failsafe” and “completely off the books” (sound familiar?).
There’s no mention of the original Helicarrier in the Age of Ultron prelude comic, nor in any other tie-in materials that I’ve read.