As fate would have it, the Thanos that exists in 2014 is eventually made aware of their plan through a convenient plot device involving Nebula's robotic parts, and that's the version of the character that serves as the villain for the remainder of the movie.

Of course, the destruction of the Thanos of “five years ago” in the “present” of the current MCU opens the door to all manner of headaches, but the simplest explanation here is that the Thanos that Thor beheaded early in the movie is still “our” Thanos, while the one defeated at the end of the movie is from a parallel universe, which might help explain why his demise doesn’t invalidate the next few years of the MCU.

Thanos overpowers Stark, Thor and a Mjolnir-wielding Rogers; he summons his army to retrieve the Stones, intent on using them to destroy the universe and create a new one.