Following the Avengers Civil War, the facility became Stark's residence after selling Avengers Tower and moving all equipment to the facility.
The New Avengers Facility previously served as a warehouse of Stark Industries owned by Howard Stark. With running of the time and Stark's death this place was abandoned until the Avengers took up residence here.
After defeating Ultron the Avengers decided to move to a new base which was formerly a Wherehouse of Stark. In 2015, Nick Fury went to the New Avengers Facility to inform Black Widow about the possible location of Bruce Banner. Meanwhile, Thor and Tony Stark said goodbye to Captain America as one returned to Asgard and the other wanted a normal life. Later, Captain America and Black Widow led the first training of the New Avengers which consisted in: Falcon, War Machine, Scarlet Witch and Vision.
A couple of months later, Falcon was in charge of protecting the New Avengers Facility. During his watch, he realized that someone had infiltrated into the facility with unknown reasons.
That someone was Scott Lang, who presented him as Ant-Man. Wilson asked Lang the reason of his infiltration; Lang replied that he only was looking for a device that he needed. That answer did not like Falcon and immediately attacked Lang, who using the skills of his suit and attack techniques that Hope showed managed to defeat an Avenger. After his defeat, Falcon asked to someone not to tell Cap about what happened
A year after the defeat of Ultron, Thadduess Ross visited the New Avengers Facility with Tony Stark and he presented the Sokovia Accords to The Avengers; Captain America, Black Widow, Falcon, Scarlet Witch, War Machine and Vision and than left to allow them to discuss the Accords among themselves and telling them, if they refuse to sign it will be seen as an act of resignation.
As The Avengers debate the Accords, Tony Stark supports the Accords with James Rhodes, Natasha Romanoff and Vision. Steve Rogers however doesn't agree with him, along with Sam Wilson and Wanda Maximoff. Later, Tony Stark confided Scarlet Witch in the facility until the Accords cool off with Vision giving her company, and also Hawkeye infiltrated the New Avengers Facility to save Scarlet Witch.
Tony Stark later arrives to the facility after The Avengers have been divided after the Avengers Civil War where Captain America, Falcon, Black Widow, Scarlet Witch, Hawkeye and Ant-Man are runaways, where he helps Rhodey after the misfire where he was parlayed. Tony than received a package, delivered by a FedEx driver from Rogers with a letter and phone apologizing to Stark for not telling him about his parents and promised to be their if he ever needed them.
Following the Avengers Civil War, the facility became Stark's residence after selling Avengers Tower and moving all equipment to the facility. The facility became Stark, Hogan, Rhodes and Vision's residence. Parker was invited to officially join the Avengers, but Parker declined the offer.
The facility appeared briefly near the start of the film when the Avengers discussed Thanos and his plans to eliminate half of the universe. After the Black Order's attack on Vision, Black Widow, Falcon, War Machine and Captain America brought Vision back to the facility to heal.
The Avengers are seen in the facility during the post-credits scene, shortly after Thanos snaps his fingers, whipping out %50 of the universe. Captain Marvel turns up and asks where Nick Fury is.
Five years after the decimation, the Avengers, including Ant-Man and Rocket, and minus Iron Man (at first) are coming up with the idea of time travel (after Scott tells them about the Quantum Realm. The tests are held at the facility, buy they aren't successful with the attempt. Tony later turns up after discovering time travel and helps them build the machine to help them time travel. After the Avengers get all the Infinity Stones from the past, Hulk snaps his fingers and brings everyone who disintegrated 5 years ago, into 2023. The facility is soon destroyed when Thanos and his army return from 2014 and the Battle of Earth is held outside the facility, which the Avengers win when Iron Man snaps his fingers, whipping out Thanos and his army once and for all, at the cost of his own life.
During the mid-credits scene, Spider-Man is seen flying through New York and flies through the Avengers Facility, which is being rebuilt and renamed when he is going to meet his girlfriend Michelle Jones, for their date.