I think you are mistaken about your sources. It is clear that Romulus and Remus quarrelled and the former killed the later. This is why Rome is called Rome; it is named after Romulus. The two best sources for this is found in Plutarch and Ovid.
Here is the story in brief. Romulus and Remus wanted to found their cities on two different sites. Romulus wanted to establish his city on the Palatine hill and Remus wanted to establish his city on the Aventine Hill. To settle the issue they decided to use augury. Remus saw eagles first, which seemed to favor him. Then Romulus saw twice that amount, which seemed to favor him. In the end, they quarrelled and Romulus won out as he killed Remus.
That said, it is possible to have alternate endings in mythology, as mythology was fluid in the ancient world. However, when it comes to Romulus and Remus the sources are pretty clear that there is only one version.