Proof.
By Sites, Lemma 7.32.7 there is a one to one correspondence between points of the site and points of the associated topos, hence it suffices to prove (1). By Sites, Proposition 7.33.3 the functor u has the following properties: (a) u(S) = \{ *\} , (b) u(U \times _ V W) = u(U) \times _{u(V)} u(W), and (c) if \{ U_ i \to U\} is an étale covering, then \coprod u(U_ i) \to u(U) is surjective. In particular, if U' \subset U is an open subscheme, then u(U') \subset u(U). Moreover, by Sites, Lemma 7.32.7 we can write u(U) = p^{-1}(h_ U^\# ), in other words u(U) is the stalk of the representable sheaf h_ U. If U = V \amalg W, then we see that h_ U = (h_ V \amalg h_ W)^\# and we get u(U) = u(V) \amalg u(W) since p^{-1} is exact.
Consider the restriction of u to S_{Zar}. By Sites, Examples 7.33.5 and 7.33.6 there exists a unique point s \in S such that for S' \subset S open we have u(S') = \{ *\} if s \in S' and u(S') = \emptyset if s \not\in S'. Note that if \varphi : U \to S is an object of S_{\acute{e}tale} then \varphi (U) \subset S is open (see Proposition 59.26.2) and \{ U \to \varphi (U)\} is an étale covering. Hence we conclude that u(U) = \emptyset \Leftrightarrow s \in \varphi (U).
Pick a geometric point \overline{s} : \overline{s} \to S lying over s, see Definition 59.29.1 for customary abuse of notation. Suppose that \varphi : U \to S is an object of S_{\acute{e}tale} with U affine. Note that \varphi is separated, and that the fibre U_ s of \varphi over s is an affine scheme over \mathop{\mathrm{Spec}}(\kappa (s)) which is the spectrum of a finite product of finite separable extensions k_ i of \kappa (s). Hence we may apply Étale Morphisms, Lemma 41.18.2 to get an étale neighbourhood (V, \overline{v}) of (S, \overline{s}) such that
U \times _ S V = U_1 \amalg \ldots \amalg U_ n \amalg W
with U_ i \to V an isomorphism and W having no point lying over \overline{v}. Thus we conclude that
u(U) \times u(V) = u(U \times _ S V) = u(U_1) \amalg \ldots \amalg u(U_ n) \amalg u(W)
and of course also u(U_ i) = u(V). After shrinking V a bit we can assume that V has exactly one point lying over s, and hence W has no point lying over s. By the above this then gives u(W) = \emptyset . Hence we obtain
u(U) \times u(V) = u(U_1) \amalg \ldots \amalg u(U_ n) = \coprod \nolimits _{i = 1, \ldots , n} u(V)
Note that u(V) \not= \emptyset as s is in the image of V \to S. In particular, we see that in this situation u(U) is a finite set with n elements.
Consider the limit
\mathop{\mathrm{lim}}\nolimits _{(V, \overline{v})} u(V)
over the category of étale neighbourhoods (V, \overline{v}) of \overline{s}. It is clear that we get the same value when taking the limit over the subcategory of (V, \overline{v}) with V affine. By the previous paragraph (applied with the roles of V and U switched) we see that in this case u(V) is always a finite nonempty set. Moreover, the limit is cofiltered, see Lemma 59.29.4. Hence by Categories, Section 4.20 the limit is nonempty. Pick an element x from this limit. This means we obtain a x_{V, \overline{v}} \in u(V) for every étale neighbourhood (V, \overline{v}) of (S, \overline{s}) such that for every morphism of étale neighbourhoods \varphi : (V', \overline{v}') \to (V, \overline{v}) we have u(\varphi )(x_{V', \overline{v}'}) = x_{V, \overline{v}}.
We will use the choice of x to construct a functorial bijective map
c : |U_{\overline{s}}| \longrightarrow u(U)
for U \in \mathop{\mathrm{Ob}}\nolimits (S_{\acute{e}tale}) which will conclude the proof. See Lemma 59.29.7 and its proof for a description of |U_{\overline{s}}|. First we claim that it suffices to construct the map for U affine. We omit the proof of this claim. Assume U \to S in S_{\acute{e}tale} with U affine, and let \overline{u} : \overline{s} \to U be an element of |U_{\overline{s}}|. Choose a (V, \overline{v}) such that U \times _ S V decomposes as in the third paragraph of the proof. Then the pair (\overline{u}, \overline{v}) gives a geometric point of U \times _ S V lying over \overline{v} and determines one of the components U_ i of U \times _ S V. More precisely, there exists a section \sigma : V \to U \times _ S V of the projection \text{pr}_ U such that (\overline{u}, \overline{v}) = \sigma \circ \overline{v}. Set c(\overline{u}) = u(\text{pr}_ U)(u(\sigma )(x_{V, \overline{v}})) \in u(U). We have to check this is independent of the choice of (V, \overline{v}). By Lemma 59.29.4 the category of étale neighbourhoods is cofiltered. Hence it suffice to show that given a morphism of étale neighbourhood \varphi : (V', \overline{v}') \to (V, \overline{v}) and a choice of a section \sigma ' : V' \to U \times _ S V' of the projection such that (\overline{u}, \overline{v'}) = \sigma ' \circ \overline{v}' we have u(\sigma ')(x_{V', \overline{v}'}) = u(\sigma )(x_{V, \overline{v}}). Consider the diagram
\xymatrix{ V' \ar[d]^{\sigma '} \ar[r]_\varphi & V \ar[d]^\sigma \\ U \times _ S V' \ar[r]^{1 \times \varphi } & U \times _ S V }
Now, it may not be the case that this diagram commutes. The reason is that the schemes V' and V may not be connected, and hence the decompositions used to construct \sigma ' and \sigma above may not be unique. But we do know that \sigma \circ \varphi \circ \overline{v}' = (1 \times \varphi ) \circ \sigma ' \circ \overline{v}' by construction. Hence, since U \times _ S V is étale over S, there exists an open neighbourhood V'' \subset V' of \overline{v'} such that the diagram does commute when restricted to V'', see Morphisms, Lemma 29.35.17. This means we may extend the diagram above to
\xymatrix{ V'' \ar[r] \ar[d]^{\sigma '|_{V''}} & V' \ar[d]^{\sigma '} \ar[r]_\varphi & V \ar[d]^\sigma \\ U \times _ S V'' \ar[r] & U \times _ S V' \ar[r]^{1 \times \varphi } & U \times _ S V }
such that the left square and the outer rectangle commute. Since u is a functor this implies that x_{V'', \overline{v}'} maps to the same element in u(U \times _ S V) no matter which route we take through the diagram. On the other hand, it maps to the elements x_{V', \overline{v}'} and x_{V, \overline{v}} in u(V') and u(V). This implies the desired equality u(\sigma ')(x_{V', \overline{v}'}) = u(\sigma )(x_{V, \overline{v}}).
In a similar manner one proves that the construction c : |U_{\overline{s}}| \to u(U) is functorial in U; details omitted. And finally, by the results of the third paragraph it is clear that the map c is bijective which ends the proof of the lemma.
\square
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