It was reported yesterday that the Dollhouse creator is in final talks to direct the picture. Variety now claims that he is also penning a new draft of Zak Penn's screenplay.
Penn has written a number of Marvel movies, including X-Men: The Last Stand, Fantastic Four and The Incredible Hulk.
Whedon has written for the Marvel comic books Runaways and Astonishing X-Men.
The Avengers is scheduled for a May 4, 2012 release.
The movie will feature Marvel heroes Iron Man (Robert Downey Jr), Captain America (Chris Evans), Thor (Chris Hemsworth) and SHIELD leader Nick Fury (Samuel L. Jackson) among others.