The Attack on the New Avengers Facility was the first assault against the Avengers after the Time Heist initiated by Thanos, who emerged from a new timeline during the Theft of the Power Stone.
After time-travelling from 2014 to 2023, Thanos obliterated the New Avengers Facility with his flagship, the Sanctuary II, shortly after the Reversal of the Decimation.
After the Avengers successfully regained the Infinity Stones from alternate timelines, Tony Stark had finished developing his own Infinity Gauntlet. Stark gave the duty to use his Gauntlet to bring back everyone who had been decimated by Thanos to Bruce Banner. Meanwhile, Nebula, who came from the past, sabotaged the Avengers' time travel device in order to bring Thanos and his armies to the present.
After Bruce Banner reversed the Decimation by snapping, Thanos and his warship had appeared outside of the New Avengers Facility and obliterated the base and its surroundings. Thanos deployed the Outriders to hunt down the Infinity Gauntlet, which was in Hawkeye's possession. Barton immediately becomes aware of the gang of Outriders chasing him in the sewers underground as he recovers the Gauntlet.
Thanos leaves his ship and rendezvous with past Nebula, praising her for her efforts, and ordering her to retrieve the stones while he sits and waits. Gamora, still on the ship, asks present Nebula what happens to them in the future, prompting Nebula to answer that she tried to kill Gamora several times but they grew to become friends and later sisters.
Realizing the error of her ways, Gamora extends her hand to Nebula, saying that they can stop Thanos. Stark wakes up Rogers and hands him back his shield, and the two meet up with Thor, who has been observing Thanos. Thor tells the two that Thanos has been sitting doing nothing for a while, and Tony tells Rogers that the stones are buried somewhere under the rubble, but Thanos does not have them, and Rogers is determined to keep it that way. As the trio prepare to battle, Thor summons a bolt of lightning and dons his battle gear, as well as summoning both Mjølnir and Stormbreaker, determined to kill Thanos properly this time.
The trio immediately confront Thanos, who goes on a monologue about their failures prompting them to return to him. Thanos announces his goal of destroying the universe as it is and using the stones to create a new universe, one that's truly grateful for the life he had given them, realizing that leaving half of the universe alive is a mistake his future self committed and that there are those who will still resist.
Captain America retorts that his new era would be built on blood, but Thanos refutes that his new universe would be blissfully unaware of the previous one. The team of Thor, Captain America and Iron Man engage in a heated battle with the Mad Titan.
Meanwhile, with the destruction of the base, the remaining Avengers were trapped under the rubble of the base, with Rhodes, Rocket and Hulk drowning due to the intense amounts of water surging into their area. Having survived the blast by shrinking, Ant-Man realized his teammates were in danger and began a rescue effort, leaping through the rubble.
As Hawkeye runs from the Outriders, he plants several explosive arrows behind him, blowing up the sewers as he runs towards an open spot. The Outriders are momentarily stunned and continue to chase Barton, who uses a zipline to reach a higher point, using his sword to bisect the Outriders jumping after him. Having killed his pursuers, Barton takes a breath until he is confronted by past Nebula and hands her the Gauntlet, believing her to be the present Nebula.
Barton then hears Nebula talk to Thanos through her communicator, confused, Nebula pins him down and prepares to shoot him, but she is confronted by Gamora and present Nebula. Gamora and present Nebula plead with past Nebula in a stand-off, saying that she can change as she is aware of what happens in the future. After hesitating, past Nebula points her gun at Gamora, prompting the present Nebula to immediately shoot her past counterpart through the heart.
During the battle against Thanos, despite the team effort and combination attacks of Thor, Rogers and Stark, they immediately lose their advantage in numbers as Thanos pushes the trio on the defensive. With Stark and Rogers knocked out, Thor duels Thanos alone, attempting to use both of his weapons.
Thor attempts to call Stormbreaker back in his hand, but Thanos catches it and tries to cut Thor with it, but the Asgardian is saved by Rogers picking up and wielding Mjølnir, with a proud Thor realizing that Rogers was always worthy. With combination attacks with Mjølnir and his shield, Rogers fights Thanos alone and manages to briefly overwhelm him; however, Thanos aggressively fights back, managing to rip Rogers' shield apart and greatly injured the Avenger.