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Let $f: X \to Y$ be a morphism between noetherian integral schemes. Suppose $f$ is finite flat of degree two. Then is there an involution $\sigma: X \to X$ over $Y$, which gives the non-trivial Galois involution at the generic point?

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Sure. Consider what happens at the level of rings $B \to A$ and attempt to define the involution there. –  Abhinav Kumar Jul 7 '13 at 23:48
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You are implicitly assuming that $f$ is generically etale. In characteristic 2, there are finite flat morphisms of degree 2 that are purely inseparable. –  Jason Starr Jul 8 '13 at 0:40
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Since it is finite flat of degree 2, Zariski-locally on the base it is ${\rm{Spec}}(A)\rightarrow{\rm{Spec}}(B)$ where 1 is part of a $B$-basis $\{1,a\}$ of $A$. If $T^2-uT+v$ is the characteristic polynomial of $a$-multiplication on $A$ then $B[T]/(T^2-uT+v)\rightarrow A$ via $X\mapsto a$ is an isomorphism. Then $T \mapsto u-T$ is an $A$-automorphism that does the job when $T^2-uT+v$ is separable over Frac($B$). –  user61789 Jul 8 '13 at 1:39
    
Good point, Jason :-) –  Abhinav Kumar Jul 8 '13 at 13:36
    
If $X$ and $Y$ are also regular then any finite generically etale morphism of degree $2$ between them is flat and $X$ is the normalization of $Y$ in the function field of $X$ (by Zariski's main theorem). It thus naturally carries an extension of the generic involution by the construction of the normalization. –  Damian Rössler Jul 8 '13 at 22:21
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