I don't know whether Alien Resurrection Special Edition should be canon or not. Unlike the Alien 3 SE there are no blatant contradictions but there are several important continuity issues. The SE has a different ending scene where the Betty lands on Earth near the ruins of Paris and Ripley and Call talk about what they're going to do. This doesn't contradict the theatrical version in terms of continuity since the SE ending scene could've happened after the theatrical ending scene but the two scenes have conflicting themes. In the theatrical version, Ripley and Call find Earth to be beautiful while in the SE they find it to be a wasteland. Also, Ripley says the line "I don't know, I'm a stranger here myself" at the end of both scenes. Although people do sometimes repeat themselves, this further implies that the two scenes were not meant to coexist.
Another issue is the introductory scenes aboard the Betty which have been completely rearranged in the SE. In the theatrical version, the first scene is the one with Elgin and Christie. At the end of the scene Elgin asks where the others are and Christie replies that they're in the cargo bay. Then comes the scene with Call and Vriess working in the cargo bay and their confrontation with Johner. Last, comes the scene with Elgin and Hillard on the bridge. In the SE, the scene with Elgin and Hillard comes first. At the end of the scene is an added bit where Elgin calls the rest of the crew over the intercom and tells them to prepare for arrival. Then it cuts to the scene with Call and Vriess working in the cargo bay. Elgin's voice is heard over the intercom as a voiceover, unlike in the theatrical version. Then comes the scene with Elgin and Christie. The bit where Elgin asks where the others are has been cut out. Last, comes the confrontation with Johner which is somewhat different from the theatrical version. In the SE Vriess throws a wrench at Johner and Call calls him an inbred motherf**ker while in the theatrical version they just exchange hurt looks. Johner says "whoa" at a different point in time. I know movies aren't always shown in chronological order (e.g. flashbacks) but this doesn't seem to be the same thing.
What do you guys think? Is it canon or not?
