[[WMG: The scientifically impossible parts were actually out-and-out [[DeusExMachina miracles]].]]

While the movie does begin with the clone protagonists having to [[OutgrownSuchSillySuperstitions outgrow the silly superstitions]] their keepers instilled in them, the story is certainly far from being a slam against ''all'' religion, and even rather friendly to ''some'' religion elsewhere. Two particular examples come to mind: the construction worker on the scaffolding after Lincoln Six Echo and Jordan Two Delta survive their pursuers' major property-wrecking attack rather enthusiastically assuring them that "Jesus must love you!" for them to have survived so improbably; later, after learning about (and trying out) the physical act of love with Lincoln, Jordan also concludes that "There really is an Island." (In other words, Heaven really does exist.)

The former example, in addition to being a bit of a LampshadeHanging on the PlotArmor that ensures their improbable survival, might well be a [[ShoutOut hat-tip]] from the creator of the movie (Creator/MichaelBay) to his own [[{{God}} Creator]]. In other words, we're being invited to think of the author of the script as being the ''Deus'' in the DeusExMachina that saves their lives. The latter example, meanwhile, reinforces the idea that, rather than simply throwing away your faith because your former god (Don Creech, billed in the credits as the "God-Like Man") proved to be a false idol, you should go find a real God. The Island, which your keepers promised you was going to be a utopia, turns out to be a scam? Then go find a real island.

Where this all leads is to a philosophical and theological explanation for how Lincoln Six Echo could possibly have obtained memories from the original Tom Lincoln despite this being scientifically impossible. Who says science has anything to do with this plot development? The reason Lincoln Echo Six remembers the boat known as the Renovatio that he shouldn't be able to is because ''Michael Bay says so''. Since Michael Bay, as the film's creator, gets well-nigh God-like powers to make anything happen that he wants, he's decided to grant his characters a miracle. By the HappyEnding, Lincoln and Jordan are on the actual boat from the late Tom Lincoln's memory, and headed out--presumably--for a real island somewhere. If they continue down the philosophical and theological path on which they've started, [[FridgeBrilliance the film is subtly telling us]], eventually they'll find the real {{God}} and real {{Heaven}} as well.

[[WMG: Tom Lincoln is [[Literature/{{Trainspotting}} Mark Renton]].]]

Rents, after he [[spoiler: scams Sick Boy at the end of Literature/{{Porno}}]] sets himself up in the US and discovers a hidden talent for design. Since Sick Boy wants revenge, he changes his name. Why he looks so young is because he avails of replacement organs already. Also, when he attacks his clone in the house, he mistakes the clone for one of his former so-called-mates out for revenge.