1999–2010
Weaving played the enigmatic and evil-minded Agent Smith in the 1999 film The Matrix. He later reprised that role in the film's 2003 sequels, The Matrix Reloaded and The Matrix Revolutions. He was a voice actor in the cartoon film The Magic Pudding.
He received additional acclaim in the role of the half-elven lord Elrond in Peter Jackson's three-film adaptation of The Lord of the Rings, released between 2001 and 2003. Weaving was the main actor in Andrew Kotatko's award-winning film Everything Goes (2004). He starred as a heroin-addicted ex-rugby league player in the 2005 Australian indie film Little Fish, opposite Cate Blanchett. Weaving played the title role as V in the 2005 film V for Vendetta, in which he was reunited with the Wachowskis, creators of The Matrix trilogy, who wrote the adapted screenplay. Actor James Purefoy was originally signed to play the role, but was fired six weeks into filming over creative differences. Weaving reshot most of Purefoy's scenes as V (even though his face is never seen) apart from a couple of minor dialogue-free scenes early in the film while stuntman David Leitch performed all of V's stunts.
Weaving reprised his role as Elrond for the video game The Lord of the Rings: The Battle for Middle-Earth II. He regularly appears in productions by the Sydney Theatre Company (STC). In 2006, he worked with Cate Blanchett on a reprise of the STC production of Hedda Gabler in New York City.
In a controversial move by director Michael Bay, Weaving was chosen as the Decepticon leader Megatron vocally in the 2007 live-action film Transformers, rather than using the original version of the character's voice created by the voice actor Frank Welker. Weaving himself was unaware of the controversy, having accepted the role based on Michael Bay's personal request; in a November 2008 Sun Herald interview, he said he had never seen Transformers. Though Weaving reprised his role in two sequels, he does not have much personal investment in the Transformers films. In February 2010, Weaving revealed to The Age: "Director Michael Bay talks to me on the phone. I've never met him. We were doing the voice for the second one and I still hadn't seen the first one. I still didn't really know who the characters were and I didn't know what anything was. It's a voice job, for sure, and people assume I've spent my life working on it, but I really know so little about it." In 2012, Weaving said to Collider: "It was one of the only things I've ever done where I had no knowledge of it, I didn't care about it, I didn't think about it. They wanted me to do it. In one way, I regret that bit. I don't regret doing it, but I very rarely do something if it's meaningless. It was meaningless to me, honestly. I don't mean that in any nasty way."
Weaving played a supporting role in Joe Johnston's 2010 remake of the 1941 film The Wolfman, starring Benicio del Toro. Immediately after Wolfman wrapped in spring 2008, he returned home to Australia to film a lead role in the film Last Ride, directed by Glendyn Ivin. In early 2009, Guillermo del Toro, then director of The Hobbit films, prequels to The Lord of the Rings, confirmed his intent to again cast Weaving as Elrond of Rivendell in a BBC interview. When asked about reprising the role, Weaving replied that he was game, but had not officially been approached. Del Toro eventually left the project; Peter Jackson decided to direct the films himself but Weaving was not officially confirmed in the cast until May 2011.
Weaving spent the summer of 2009 starring in the Melbourne Theatre Company's production of God of Carnage, portraying the caustic lawyer Alain Reille. He returned to the stage in November 2010 in Sydney Theatre Company's Uncle Vanya, co-starring Cate Blanchett and Richard Roxburgh. Weaving filmed a guest role on Roxburgh's Australian TV series Rake in May 2010.
In May 2009, Weaving accepted a co-starring role in the docudrama Oranges and Sunshine, about the forced migration of thousands of British children to Australia in the 1950s. Filming began in autumn 2009 in Nottingham, England, and Adelaide, South Australia, and continued through January 2010. The film premiered at the Rome International Film Festival on 28 October 2010 and garnered positive reviews. 2010 saw the release of Legend of the Guardians (formerly The Guardians of Ga'Hoole), in which Weaving has another high-profile voice role, portraying two different owls named Noctus and Grimble in Zack Snyder's film adaptation of Kathryn Lasky's popular series of children's books.
On 4 May 2010, it was officially confirmed by Marvel Studios that Weaving would play the Nazi supervillain Johann Schmidt / Red Skull in the superhero film Captain America: The First Avenger. Weaving completed filming his role on the project in September 2010 and returned to Sydney to prepare for Uncle Vanya. It is unlikely he will sign on for any further installments in the Marvel Cinematic Universe (MCU); in an August 2011 Baltimore Sun interview, the actor confided he is weary of typecasting and of "blockbuster" films in general: "I think I've about had enough... I'm not sure how many more of them I'll make. It doesn't feel to me as though they've been the majority of my work, though that's probably the way it seems to most other people." Red Skull returned in the MCU films Avengers: Infinity War (2018) and Avengers: Endgame (2019), with Ross Marquand replacing Weaving in the role.