What version of the Omnidroid attacks the city at the end?

The version of the Omnidroid that attacks the city at the end is Omnidroid v10.

Syndrome deploys this final machine to Metroville as the centerpiece of Operation Kronos. His plan is to let the robot devastate the city, then defeat it publicly with his remote-control gauntlet and appear to be a superhero. The Omnidroid’s artificial intelligence instead recognizes the remote as a threat, disarms Syndrome, and turns against him.

The Incredibles and Frozone then battle the robot. Its size, strength, learning ability, rocket-powered claws, and multiple legs make it more dangerous than the earlier prototypes. The family eventually uses Syndrome’s remote to control one of the Omnidroid’s own weapons. Elastigirl launches a detached claw through its armored shell, destroying its power source.

A common mix-up is confusing the city battle with Bob’s earlier island mission, where he fights an earlier Omnidroid prototype. The climactic Metroville attack specifically involves v10, the final model shown in the film.