Would the experience be one of Spielbergian wonder, all diffused light and magical bike rides, or a nightmare of abduction and anal probes?

The comedy “Paul” posits another option: Perhaps the alien, who calls himself Paul, is a potty-mouthed, potsmoking space traveler flummoxed by all these human fears of anal probes.

“Am I harvesting farts?” Paul says with exasperation. “How much can I learn from an ass?” The question is meant rhetorically, but it summarizes the challenges inherent in the movie, because “Paul” is a mess. Its tone is uneven, jarringly so, and weighed down by jokes as flat as the top of Devil’s Tower. But somehow, its earthly limitations matter less than its earthy heart.

That’s not surprising given the pedigree involved. Written by and starring Simon Pegg and Nick Frost (“Shaun of the Dead,” “Hot Fuzz”), the film is an affectionate send-up of sci-fi from the 1970s and ’80s. Their riffing is leant an unexpected depth by director Greg Mottola, who brought similar sensitivity to “Superbad” and “Adventureland.”

In this seeming mishmash, Pegg and Frost are Graeme and Clive, British comic-book nerds who rent an RV to visit Area 51 and other American hot spots of UFO lore. They quickly get more than they bargained for when they see a car careen off the highway and crash in the desert. Its sole occupant is a familiar-looking spaceman (voiced by Seth Rogen, “The Green Hornet”).

The little green man tells the astonished pair he is escaping his toplevel U.S. captors after 60 years under the misimpression that he was their guest, and not a prisoner. In short order, they wind up joined by Ruth (Kristen Wiig, TV’s “Saturday Night Live”), a fundamentalist Christian whose belief system is smashed by Paul’s existence.

So begins a road trip in which the motley group is pursued by government agents (including Jason Bateman, “The Switch,” and “SNL”’s Bill Hader) and Ruth’s crazed, Biblethumping father (John Carroll Lynch, “Shutter Island”). Bonding and romance bloom.

The results are a mixed bag. Paul is a marvel of CG animation, and Rogen delivers a voice performance more nuanced than most of his on-screen portrayals. But a script that equates references with jokes compromises such ingenuity. Nods to “Star Wars,” “Close Encounters,” “Alien” and the like simply let us know the filmmakers have seen the same movies that we have. Despite a generally sweet disposition, “Paul” turns cringingly ham-fisted in its denunciation of religion.

But then it can turn around and surprise. Late in the picture, Blythe Danner (“Little Fockers”) appears as an older woman whose life was devastated after she found Paul when she was a little girl. The ensuing scene is remarkable and poignant, enveloped in layers of guilt, regret and, finally, a wide-eyed return to childlike wonder.

In the end, “Paul” is not stellar, but in such moments, it can brush the heavens.