In the earlier days of the Marvel Cinematic Universe, most villains were "one-and-done," only appearing in a single film before getting killed off. That was the case for many villains such as Ultron and Whiplash. Ever since Phase Three, however, it seems as if Marvel is taking a shift in its approach, with such antagonists as Baron Zemo and The Mandarin now set to appear in future projects.
With that new approach, it's not impossible for a major threat like Ultron, who was presumed dead, to be brought back to the forefront. Here are three possible ways for Ultron to make a return to the MCU.
The Government Had an Ultron Copy
In Spider-Man: Homecoming, Peter Parker becomes stuck inside the U.S. government's Damage Control warehouse, where he finds and picks up an Ultron head. Seeing that Stark Industries was a major stakeholder in Damage Control, that would mean that both the government and Tony Stark have a copy of what seems to be a once-functioning Ultron drone.
There is some speculation, however, that the head could perhaps actually belong to the original Ultron as the head's eyes were glowing red. The only times that we saw that in Ultron was when it was alive and contained its consciousness. With Stark gone, it would be a risky move for an agency like S.W.O.R.D. to conduct research on potentially active Ultron remains, as one wrong move could jump-start the android back to life.
An Ultron Drone Survived
After the Battle of Sokovia, Vision destroys the final remaining Ultron drone. However, what if that was not the last one and another survived? When the Avengers were rescuing civilians in Sokovia, at one point Captain America throws a drone off of a bridge after the city began lifting into the air. Despite being easily torn apart by the Avengers, the Ultron drones are surprisingly durable. Some of the drones were shown taking multiple hits from super-powered beings before being destroyed, and since the drone was not shown to have "died" before it was knocked off, it would not be too far fetched to think that it could have survived a long fall.
Amidst all of the chaos and cleanup following the battle, the damaged drone could have easily slipped away without alerting the Avengers, laying low before eventually encountering an antagonistic group such as A.I.M. or remaining Hydra loyalists. Another possibility could be the damaged drone falling into the hands of Latveria, an Eastern European country led in the comics by Doctor Doom. Having a functioning Ultron in his arsenal would definitely capture the attention of the Avengers and could be one way to introduce the supervillain into the MCU.
Backup Code Gone Wrong
With Tony Stark gone, it is possible that Bruce Banner, Nick Fury or one of the other Avengers would go through his old research to recover information that could help stop future threats. Being scientists, it is likely that Stark and Banner would have had an unfinished backup copy of Ultron's programming from when they first started the project. With J.A.R.V.I.S. no longer there to contain Ultron, any tampering of Ultron's code would risk releasing the robot back onto the internet, at which point it could spread and rebuild itself.
A common criticism of the MCU Ultron is that he is not menacing enough and has a lot of similarities to Tony Stark. This can be explained by Stark and Banner using their own brains as a reference point when constructing Ultron. Without Stark's presence, however, it could be possible for this new and slightly incomplete Ultron to lack the humor that existed in the original and be much more dark and menacing like he was in the comics. If Marvel really wanted to stay true to the source, it could even have Hank Pym be the one to accidentally restart Ultron's code, as Pym was the one who created Ultron in the comics.