How did this work exactly? There's a pretty significant number of personnel required to keep an aircraft carrier running, let alone one that can fly and has cloaking technology. Is there an official explanation as to how Hawkeye (and company) was able to fly a Quinjet right up to the Helicarrier, clearly within visual range of flight deck staff and launch an attack? Didn't Tony Stark have Jarvis stealing all of SHIELD's intelligence after he boarded? Wouldn't this have enabled him to extrapolate weaknesses in the Helicarrier's defense systems?
Is there an official explanation as to how Hawkeye (and company) was able to fly a Quinjet right up to the Helicarrier, clearly within visual range of flight deck staff and launch an attack?
It was a False Flag attack, meaning they pretended to be good Shield Agents prior to setting off the explosion. The jet was spotted by the Helicarrier, and radioed for their clearance to be cleared to approach. (Mixed Script and Transcript)
[INT. AIRCRAFT CARRIER, DAY: Outside the HELICARRIER, a lone carrier slowly hovers over the ship.]
SHIELD BASE VOICE: Transport Six-Six-Bravo, please relay confirm codes. I've got you on the computer, but not on the day log. What is your haul? Over.
BARTON: Arms and ammunition. Over.
[Inside, BARTON and his crew suit up and arm themselves. Barton pulls out his hi-tech bow and arrows.]
So they were noticed, but between the correct codes, a valid ship/markings, human error/leeway, etc, they were cleared as a valid ship. Tricking a low level guard or comm officer should be easy for a master spy/assassin like Clint.
Even inside the Helicarrier, they attempted to blend in (From the transcript).
AGENT JASPER SITWELL (V.O.): We got perimeter breach! Hostiles are in S.H.I.E.L.D. Gear. Call-outs at every junction.
Call-outs meaning known agents must announce who they are and be wary instead of trusting uniforms, in the maze that is a ship's interior.
A little later (from the script):
On the other side, BARTON'S men enter the port side. CAPTAIN AMERICA looks down, pondering if they are help. Evidently not as they begin SHOOTING at him and throwing grenades. CAPTAIN AMERICA jumps to the other railing and down with Barton's men. He begins to TAKE THEM DOWN, even goes as far as throwing one off. A few more enter, FIRING. CAPTAIN AMERICA grabs a NOVESKE RIFLEWORKS DIPLOMAT (big word for big fuckin' gun) and jumps back up to his position, firing down at them.
Also, they are in the air. There was no flight crew on deck to see anything hinky happening. Even if they could see, it only took Barton seconds to aim and launch the arrow, then trigger the explosive.
Didn't Tony Stark have Jarvis stealing all of SHIELD's intelligence after he boarded?
At the time, Stark was looking for evidence on SHIELD's goals, not external sensors. Even if he did, Stark seemed to be manually going through the data, and he would have no reason to suspect the incoming jet was a false friendly. AND The Helicarrier is a top secret military installation, that can MOVE and Cloak. None had any reason to think they could be targeted. Hubris. Furthermore, the main Antagonists, Fury, Stark, Cap, etc, are too busy fighting amongst themselves while trying to figure out Loki's plans to pay enough attention. Ironically, they were playing directly into Loki's plans when it happened.
The later movies, specifically Captain America 2: Winter Soldier show that Fury and S.H.I.E.L.D. is not as well informed as they would like, failing to see multiple false flag/double agent attacks. Agent Jasper Sitwell, who in The Avengers worked to stop the false flag attack by the compromised Clint Barton and his men, turned out to be a HYDRA agent himself.