In the Ultimate Marvel universe, the Triskelion is the island headquarters of S.H.I.E.L.D. and formerly inhabited by the Ultimates. The Triskelion's architectural design was planned and layout by architect Frank Gehry. The Triskelion was originally designed by British architect Norman Foster and planned to have mobility like the Helicarrier, but never came to be due to monetary problems. The Triskelion was partially, but significantly, destroyed by the Liberators when its super-soldiers pushed and scuttled the S.H.I.E.L.D. Helicarrier onto the facility, which the Scarlet Witch (who was present in Nick Fury's office) used her powers in saving only the first three floors of the building and everyone within them.
During the Ultimatum storyline, the Triskelion was attacked by suicide-bomber duplicates of Multiple Man until Hank Pym sacrificed himself in stopping the clones. Shortly following the events of Ultimatum, the Triskelion was undergoing another stage of repairs and became the headquarters of the Ultimates' replacements, the Avengers.
During the Avengers' tenure, the Triskelion was attacked by vampires, in which the subsequent battle resulted with the entire facility being teleported to the middle of a desert in Iran. The presence of the Triskelion caused some vocal concerns from the Iranian government, in which S.H.I.E.L.D. temporarily relocated their headquarters to Stark Industries. With help from the European Defense Initiative, S.H.I.E.L.D. was trying to find a way to return the Triskelion back to New York.
This Triskelion was finally left to the new pro-American, Iranian government after powered rebels had taken down the former rulers, as the way to threaten Russia, China, and the Arabic nations authorities.
A new Triskelion was built in New York, and in other countries, such as one in Bangkok in SEAR (South East Asian Republic, another newly established superhuman-run state).
The Triskelion in New York City was destroyed when Hulk escaped custody along with Reed Richards, but was rebuilt into a flying fortress using technology from Richards' Aleph-One.
As part of the All-New, All-Different Marvel event, the Earth-616 version of the Triskelion debuts. It is located off the coast of Manhattan. Each of the Triskelion's three wings serve a different purpose where each of them radiate from the central hub. The first wing is the home of the ground crew for the Alpha Flight Space Program. The second wing acts like the Wakandan Embassy. The third wing is the headquarters of the Earth-616 version of the Ultimates.
The Triskelion is mentioned by Jemma Simmons in the TV series Agents of S.H.I.E.L.D. in episode "The Hub" and in search files in the episode "T.A.H.I.T.I." It is also later referenced in "End of the Beginning" when Jasper Sitwell receives orders to board the Lemurian Star.
The Triskelion appears in the 2014 film Captain America: The Winter Soldier as S.H.I.E.L.D.'s Washington D.C. headquarters, where it is located on Theodore Roosevelt Island at the foot of the Roosevelt Bridge. The Triskelion was taken over by Alexander Pierce who used the ships to try and eliminate people that Hydra deemed a threat to society. It is destroyed in that film by a disabled Helicarrier (an event later referenced by Victoria Hand in the Agents of S.H.I.E.L.D. episode "Turn, Turn, Turn").
In a flashback at the start of the film Ant-Man, the Triskelion is shown to be incomplete yet already functioning as S.H.I.E.L.D's headquarters when Hank Pym resigns his position in 1989.
The Triskelion is seen in Ultimate Spider-Man: Web Warriors episode "New Warriors". It is mentioned to be where the S.H.I.E.L.D. Academy is. In the episode "S.H.I.E.L.D. Academy," the Triskelion's S.H.I.E.L.D. Academy has Robert Frank as it's teacher with Captain America and Hawkeye as guest instructors. It is also shown to be somewhere off the coast of Manhattan. Arnim Zola's robotic body was found held within the Triskelion. In "Attack of the Synthezoids," Arnim Zola resurfaces and takes control of the personnel and students at the Triskelion. By the end of the episode, Arnim Zola uses the Tri-Carrier's missiles to destroy the Triskelion as Spider-Man plans to lead Agent Venom, Cloak, and Rhino into rescuing everyone from Arnim Zola. In "The Revenge of Arnim Zola," the Triskelion is rebuilt following Arnim Zola's defeat.
The Triskelion appears in Hulk and the Agents of S.M.A.S.H. episode "Planet Monster" Pt. 1. It is revealed to be where the holding cells of Leader and Ronan the Accuser is. The Supreme Intelligence sends his Kree soldiers into storming the Triskelion into freeing Ronan the Accuser. The Kree succeed in their mission, but are convinced by Leader to bring him along as well.
In the video game Ultimate Spider-Man a number of posters depicting The Triskelion are seen announcing a movie called The Ultimates, some of which include reference to a sequel by the inclusion of the number 2.
The Triskelion is featured in the video game Spider-Man: Shattered Dimensions. Ultimate Spider-Man fights Carnage here as he infects the inmates of the Triskelion's prison with Symbiotes.