Lemma 81.14.1. Let S be a scheme. Let X \to Y be a morphism of algebraic spaces over S. If (U \subset X, f : V \to X) is an elementary distinguished square such that U \to Y and V \to Y are separated and U \times _ X V \to U \times _ Y V is closed, then X \to Y is separated.
81.14 Compactifications
This section is the analogue of More on Flatness, Section 38.33. The theorem in this section is the main theorem in [CLO].
Let B be a quasi-compact and quasi-separated algebraic space over some base scheme S. We will say an algebraic space X over B has a compactification over B or is compactifyable over B if there exists a quasi-compact open immersion X \to \overline{X} into an algebraic space \overline{X} proper over B. If X has a compactification over B, then X \to B is separated and of finite type. The main theorem of this section is that the converse is true as well.
Proof. We have to check that \Delta : X \to X \times _ Y X is a closed immersion. There is an étale covering of X \times _ Y X given by the four parts U \times _ Y U, U \times _ Y V, V \times _ Y U, and V \times _ Y V. Observe that (U \times _ Y U) \times _{(X \times _ Y X), \Delta } X = U, (U \times _ Y V) \times _{(X \times _ Y X), \Delta } X = U \times _ X V, (V \times _ Y U) \times _{(X \times _ Y X), \Delta } X = V \times _ X U, and (V \times _ Y V) \times _{(X \times _ Y X), \Delta } X = V. Thus the assumptions of the lemma exactly tell us that \Delta is a closed immersion. \square
Lemma 81.14.2. Let S be a scheme. Let X be a quasi-compact and quasi-separated algebraic space over S. Let U \subset X be a quasi-compact open.
If Z_1, Z_2 \subset X are closed subspaces of finite presentation such that Z_1 \cap Z_2 \cap U = \emptyset , then there exists a U-admissible blowing up X' \to X such that the strict transforms of Z_1 and Z_2 are disjoint.
If T_1, T_2 \subset |U| are disjoint constructible closed subsets, then there is a U-admissible blowing up X' \to X such that the closures of T_1 and T_2 are disjoint.
Proof. Proof of (1). The assumption that Z_ i \to X is of finite presentation signifies that the quasi-coherent ideal sheaf \mathcal{I}_ i of Z_ i is of finite type, see Morphisms of Spaces, Lemma 67.28.12. Denote Z \subset X the closed subspace cut out by the product \mathcal{I}_1 \mathcal{I}_2. Observe that Z \cap U is the disjoint union of Z_1 \cap U and Z_2 \cap U. By Divisors on Spaces, Lemma 71.19.5 there is a U \cap Z-admissible blowup Z' \to Z such that the strict transforms of Z_1 and Z_2 are disjoint. Denote Y \subset Z the center of this blowing up. Then Y \to X is a closed immersion of finite presentation as the composition of Y \to Z and Z \to X (Divisors on Spaces, Definition 71.19.1 and Morphisms of Spaces, Lemma 67.28.2). Thus the blowing up X' \to X of Y is a U-admissible blowing up. By general properties of strict transforms, the strict transform of Z_1, Z_2 with respect to X' \to X is the same as the strict transform of Z_1, Z_2 with respect to Z' \to Z, see Divisors on Spaces, Lemma 71.18.3. Thus (1) is proved.
Proof of (2). By Limits of Spaces, Lemma 70.14.1 there exists a finite type quasi-coherent sheaf of ideals \mathcal{J}_ i \subset \mathcal{O}_ U such that T_ i = V(\mathcal{J}_ i) (set theoretically). By Limits of Spaces, Lemma 70.9.8 there exists a finite type quasi-coherent sheaf of ideals \mathcal{I}_ i \subset \mathcal{O}_ X whose restriction to U is \mathcal{J}_ i. Apply the result of part (1) to the closed subspaces Z_ i = V(\mathcal{I}_ i) to conclude. \square
Lemma 81.14.3. Let S be a scheme. Let f : X \to Y be a proper morphism of quasi-compact and quasi-separated algebraic spaces over S. Let V \subset Y be a quasi-compact open and U = f^{-1}(V). Let T \subset |V| be a closed subset such that f|_ U : U \to V is an isomorphism over an open neighbourhood of T in V. Then there exists a V-admissible blowing up Y' \to Y such that the strict transform f' : X' \to Y' of f is an isomorphism over an open neighbourhood of the closure of T in |Y'|.
Proof. Let T' \subset |V| be the complement of the maximal open over which f|_ U is an isomorphism. Then T', T are closed in |V| and T \cap T' = \emptyset . Since |V| is a spectral topological space (Properties of Spaces, Lemma 66.15.2) we can find constructible closed subsets T_ c, T'_ c of |V| with T \subset T_ c, T' \subset T'_ c such that T_ c \cap T'_ c = \emptyset (choose a quasi-compact open W of |V| containing T' not meeting T and set T_ c = |V| \setminus W, then choose a quasi-compact open W' of |V| containing T_ c not meeting T' and set T'_ c = |V| \setminus W'). By Lemma 81.14.2 we may, after replacing Y by a V-admissible blowing up, assume that T_ c and T'_ c have disjoint closures in |Y|. Let Y_0 be the open subspace of Y corresponding to the open |Y| \setminus \overline{T}'_ c and set V_0 = V \cap Y_0, U_0 = U \times _ V V_0, and X_0 = X \times _ Y Y_0. Since U_0 \to V_0 is an isomorphism, we can find a V_0-admissible blowing up Y'_0 \to Y_0 such that the strict transform X'_0 of X_0 maps isomorphically to Y'_0, see More on Morphisms of Spaces, Lemma 76.39.4. By Divisors on Spaces, Lemma 71.19.3 there exists a V-admissible blow up Y' \to Y whose restriction to Y_0 is Y'_0 \to Y_0. If f' : X' \to Y' denotes the strict transform of f, then we see what we want is true because f' restricts to an isomorphism over Y'_0. \square
Lemma 81.14.4. Let S be a scheme. Consider a diagram
of quasi-compact and quasi-separated algebraic spaces over S. Assume
f is proper,
V is a quasi-compact open of Y, U = f^{-1}(V),
B \subset V and A \subset U are closed subspaces,
f|_ A : A \to B is an isomorphism, and f is étale at every point of A.
Then there exists a V-admissible blowing up Y' \to Y such that the strict transform f' : X' \to Y' satisfies: for every geometric point \overline{a} of the closure of |A| in |X'| there exists a quotient \mathcal{O}_{X', \overline{a}} \to \mathcal{O} such that \mathcal{O}_{Y', f'(\overline{a})} \to \mathcal{O} is finite flat.
As you can see from the proof, more is true, but the statement is already long enough and this will be sufficient later on.
Proof. Let T' \subset |U| be the complement of the maximal open on which f|_ U is étale. Then T' is closed in |U| and disjoint from |A|. Since |U| is a spectral topological space (Properties of Spaces, Lemma 66.15.2) we can find constructible closed subsets T_ c, T'_ c of |U| with |A| \subset T_ c, T' \subset T'_ c such that T_ c \cap T'_ c = \emptyset (see proof of Lemma 81.14.3). By Lemma 81.14.2 there is a U-admissible blowing up X_1 \to X such that T_ c and T'_ c have disjoint closures in |X_1|. Let X_{1, 0} be the open subspace of X_1 corresponding to the open |X_1| \setminus \overline{T}'_ c and set U_0 = U \cap X_{1, 0}. Observe that the scheme theoretic image \overline{A}_1 \subset X_1 of A is contained in X_{1, 0} by construction.
After replacing Y by a V-admissible blowing up and taking strict transforms, we may assume X_{1, 0} \to Y is flat, quasi-finite, and of finite presentation, see More on Morphisms of Spaces, Lemmas 76.39.1 and 76.37.3. Consider the commutative diagram
of scheme theoretic images. The morphism \overline{A}_1 \to \overline{A} is surjective because it is proper and hence the scheme theoretic image of \overline{A}_1 \to \overline{A} must be equal to \overline{A} and then we can use Morphisms of Spaces, Lemma 67.40.8. The statement on étale local rings follows by choosing a lift of the geometric point \overline{a} to a geometric point \overline{a}_1 of \overline{A}_1 and setting \mathcal{O} = \mathcal{O}_{X_1, \overline{a}_1}. Namely, since X_1 \to Y is flat and quasi-finite on X_{1, 0} \supset \overline{A}_1, the map \mathcal{O}_{Y', f'(\overline{a})} \to \mathcal{O}_{X_1, \overline{a}_1} is finite flat, see Algebra, Lemmas 10.156.3 and 10.153.3. \square
Lemma 81.14.5. Let S be a scheme. Let X \to B and Y \to B be morphisms of algebraic spaces over S. Let U \subset X be an open subspace. Let V \to X \times _ B Y be a quasi-compact morphism whose composition with the first projection maps into U. Let Z \subset X \times _ B Y be the scheme theoretic image of V \to X \times _ B Y. Let X' \to X be a U-admissible blowup. Then the scheme theoretic image of V \to X' \times _ B Y is the strict transform of Z with respect to the blowing up.
Proof. Denote Z' \to Z the strict transform. The morphism Z' \to X' induces a morphism Z' \to X' \times _ B Y which is a closed immersion (as Z' is a closed subspace of X' \times _ X Z by definition). Thus to finish the proof it suffices to show that the scheme theoretic image Z'' of V \to Z' is Z'. Observe that Z'' \subset Z' is a closed subspace such that V \to Z' factors through Z''. Since both V \to X \times _ B Y and V \to X' \times _ B Y are quasi-compact (for the latter this follows from Morphisms of Spaces, Lemma 67.8.9 and the fact that X' \times _ B Y \to X \times _ B Y is separated as a base change of a proper morphism), by Morphisms of Spaces, Lemma 67.16.3 we see that Z \cap (U \times _ B Y) = Z'' \cap (U \times _ B Y). Thus the inclusion morphism Z'' \to Z' is an isomorphism away from the exceptional divisor E of Z' \to Z. However, the structure sheaf of Z' does not have any nonzero sections supported on E (by definition of strict transforms) and we conclude that the surjection \mathcal{O}_{Z'} \to \mathcal{O}_{Z''} must be an isomorphism. \square
Lemma 81.14.6. Let S be a scheme. Let B be a quasi-compact and quasi-separated algebraic space over S. Let U be an algebraic space of finite type and separated over B. Let V \to U be an étale morphism. If V has a compactification V \subset Y over B, then there exists a V-admissible blowing up Y' \to Y and an open V \subset V' \subset Y' such that V \to U extends to a proper morphism V' \to U.
Proof. Consider the scheme theoretic image Z \subset Y \times _ B U of the “diagonal” morphism V \to Y \times _ B U. If we replace Y by a V-admissible blowing up, then Z is replaced by the strict transform with respect to this blowing up, see Lemma 81.14.5. Hence by More on Morphisms of Spaces, Lemma 76.39.4 we may assume Z \to Y is an open immersion. If V' \subset Y denotes the image, then we see that the induced morphism V' \to U is proper because the projection Y \times _ B U \to U is proper and V' \cong Z is a closed subspace of Y \times _ B U. \square
The following lemma is formulated for finite type separated algebraic spaces over a finite type algebraic space over \mathbf{Z}. The version for quasi-compact and quasi-separated algebraic spaces is true as well (with essentially the same proof), but will be trivially implied by the main theorem in this section. We strongly urge the reader to read the proof of this lemma in the case of schemes first.
Lemma 81.14.7. Let B be an algebraic space of finite type over \mathbf{Z}. Let U be an algebraic space of finite type and separated over B. Let (U_2 \subset U, f : U_1 \to U) be an elementary distinguished square. Assume U_1 and U_2 have compactifications over B and U_1 \times _ U U_2 \to U has dense image. Then U has a compactification over B.
Proof. Choose a compactification U_ i \subset X_ i over B for i = 1, 2. We may assume U_ i is scheme theoretically dense in X_ i. We may assume there is an open V_ i \subset X_ i and a proper morphism \psi _ i : V_ i \to U extending U_ i \to U, see Lemma 81.14.6. Picture
Denote Z_1 \subset U the reduced closed subspace corresponding to the closed subset |U| \setminus |U_2|. Recall that f^{-1}Z_1 is a closed subspace of U_1 mapping isomorphically to Z_1. Denote Z_2 \subset U the reduced closed subspace corresponding to the closed subset |U| \setminus \mathop{\mathrm{Im}}(|f|) = |U_2| \setminus \mathop{\mathrm{Im}}(|U_1 \times _ U U_2| \to |U_2|). Thus we have
set theoretically. Denote Z_{i, i} \subset V_ i the inverse image of Z_ i under \psi _ i. Observe that \psi _2 is an isomorphism over an open neighbourhood of Z_2. Observe that Z_{1, 1} = \psi _1^{-1}Z_1 = f^{-1}Z_1 \amalg T for some closed subspace T \subset V_1 disjoint from f^{-1}Z_1 and furthermore \psi _1 is étale along f^{-1}Z_1. Denote Z_{i, j} \subset V_ i the inverse image of Z_ j under \psi _ i. Observe that \psi _ i : Z_{i, j} \to Z_ j is a proper morphism. Since Z_ i and Z_ j are disjoint closed subspaces of U, we see that Z_{i, i} and Z_{i, j} are disjoint closed subspaces of V_ i.
Denote \overline{Z}_{i, i} and \overline{Z}_{i, j} the scheme theoretic images of Z_{i, i} and Z_{i, j} in X_ i. We recall that |Z_{i, j}| is dense in |\overline{Z}_{i, j}|, see Morphisms of Spaces, Lemma 67.17.7. After replacing X_ i by a V_ i-admissible blowup we may assume that \overline{Z}_{i, i} and \overline{Z}_{i, j} are disjoint, see Lemma 81.14.2. We assume this holds for both X_1 and X_2. Observe that this property is preserved if we replace X_ i by a further V_ i-admissible blowup. Hence we may replace X_1 by another V_1-admissible blowup and assume |\overline{Z}_{1, 1}| is the disjoint union of the closures of |T| and |f^{-1}Z_1| in |X_1|.
Set V_{12} = V_1 \times _ U V_2. We have an immersion V_{12} \to X_1 \times _ B X_2 which is the composition of the closed immersion V_{12} = V_1 \times _ U V_2 \to V_1 \times _ B V_2 (Morphisms of Spaces, Lemma 67.4.5) and the open immersion V_1 \times _ B V_2 \to X_1 \times _ B X_2. Let X_{12} \subset X_1 \times _ B X_2 be the scheme theoretic image of V_{12} \to X_1 \times _ B X_2. The projection morphisms
are proper as X_1 and X_2 are proper over B. If we replace X_1 by a V_1-admissible blowing up, then X_{12} is replaced by the strict transform with respect to this blowing up, see Lemma 81.14.5.
Denote \psi : V_{12} \to U the compositions \psi = \psi _1 \circ p_1|_{V_{12}} = \psi _2 \circ p_2|_{V_{12}}. Consider the closed subspace
The morphism p_1|_{V_{12}} : V_{12} \to V_1 is an isomorphism over an open neighbourhood of Z_{1, 2} because \psi _2 : V_2 \to U is an isomorphism over an open neighbourhood of Z_2 and V_{12} = V_1 \times _ U V_2. By Lemma 81.14.3 there exists a V_1-admissible blowing up X_1' \to X_1 such that the strict transform p'_1 : X'_{12} \to X'_1 of p_1 is an isomorphism over an open neighbourhood of the closure of |Z_{1, 2}| in |X'_1|. After replacing X_1 by X'_1 and X_{12} by X'_{12} we may assume that p_1 is an isomorphism over an open neighbourhood of |\overline{Z}_{1, 2}|.
The result of the previous paragraph tells us that
where the intersection taken in X_1 \times _ B X_2. Namely, the inverse image p_1^{-1}\overline{Z}_{1, 2} in X_{12} maps isomorphically to \overline{Z}_{1, 2}. In particular, we see that |Z_{12, 2}| is dense in |p_1^{-1}\overline{Z}_{1, 2}|. Thus p_2 maps |p_1^{-1}\overline{Z}_{1, 2}| into |\overline{Z}_{2, 2}|. Since |\overline{Z}_{2, 2}| \cap |\overline{Z}_{2, 1}| = \emptyset we conclude.
It turns out that we need to do one additional blowing up before we can conclude the argument. Namely, let V_2 \subset W_2 \subset X_2 be the open subspace with underlying topological space
Since p_2(p_1^{-1}\overline{Z}_{1, 2}) is contained in W_2 (see above) we see that replacing X_2 by a W_2-admissible blowup and X_{21} by the corresponding strict transform will preserve the property of p_1 being an isomorphism over an open neighbourhood of \overline{Z}_{1, 2}. Since \overline{Z}_{2, 1} \cap W_2 = \overline{Z}_{2, 1} \cap V_2 = Z_{2, 1} we see that Z_{2, 1} is a closed subspace of W_2 and V_2. Observe that V_{12} = V_1 \times _ U V_2 = p_1^{-1}(V_1) = p_2^{-1}(V_2) as open subspaces of X_{12} as it is the largest open subspace of X_{12} over which the morphism \psi : V_{12} \to U extends; details omitted1. We have the following equalities of closed subspaces of V_{12}:
Here and below we use the slight abuse of notation of writing p_2 in stead of the restriction of p_2 to V_{12}, etc. Since p_2^{-1}(Z_{2, 1}) is a closed subspace of p_2^{-1}(W_2) as Z_{2, 1} is a closed subspace of W_2 we conclude that also p_1^{-1}f^{-1}Z_1 is a closed subspace of p_2^{-1}(W_2). Finally, the morphism p_2 : X_{12} \to X_2 is étale at points of p_1^{-1}f^{-1}Z_1 as \psi _1 is étale along f^{-1}Z_1 and V_{12} = V_1 \times _ U V_2. Thus we may apply Lemma 81.14.4 to the morphism p_2 : X_{12} \to X_2, the open W_2, the closed subspace Z_{2, 1} \subset W_2, and the closed subspace p_1^{-1}f^{-1}Z_1 \subset p_2^{-1}(W_2). Hence after replacing X_2 by a W_2-admissible blowup and X_{12} by the corresponding strict transform, we obtain for every geometric point \overline{y} of the closure of |p_1^{-1}f^{-1}Z_1| a local ring map \mathcal{O}_{X_{12}, \overline{y}} \to \mathcal{O} such that \mathcal{O}_{X_2, p_2(\overline{y})} \to \mathcal{O} is finite flat.
Consider the algebraic space
and with T \subset V_1 as in the first paragraph the algebraic space
obtained by pushout, see Lemma 81.9.2. Let us apply Lemma 81.14.1 to see that W_ i \to B is separated. First, U \to B and X_ i \to B are separated. Let us check the quasi-compact immersion U_ i \to U \times _ B (X_ i \setminus \overline{Z}_{i, j}) is closed using the valuative criterion, see Morphisms of Spaces, Lemma 67.42.1. Choose a valuation ring A over B with fraction field K and compatible morphisms (u, x_ i) : \mathop{\mathrm{Spec}}(A) \to U \times _ B X_ i and u_ i : \mathop{\mathrm{Spec}}(K) \to U_ i. Since \psi _ i is proper, we can find a unique v_ i : \mathop{\mathrm{Spec}}(A) \to V_ i compatible with u and u_ i. Since X_ i is proper over B we see that x_ i = v_ i. If v_ i does not factor through U_ i \subset V_ i, then we conclude that x_ i maps the closed point of \mathop{\mathrm{Spec}}(A) into Z_{i, j} or T when i = 1. This finishes the proof because we removed \overline{Z}_{i, j} and \overline{T} in the construction of W_ i.
On the other hand, for any valuation ring A over B with fraction field K and any morphism
over B, we claim that after replacing A by an extension of valuation rings, there is an i and an extension of \gamma to a morphism h_ i : \mathop{\mathrm{Spec}}(A) \to W_ i. Namely, we first extend \gamma to a morphism g_2 : \mathop{\mathrm{Spec}}(A) \to X_2 using the valuative criterion of properness. If the image of g_2 does not meet \overline{Z}_{2, 1}, then we obtain our morphism into W_2. Otherwise, denote \overline{z} \in \overline{Z}_{2, 1} a geometric point lying over the image of the closed point under g_2. We may lift this to a geometric point \overline{y} of X_{12} in the closure of |p_1^{-1}f^{-1}Z_1| because the map of spaces |p_1^{-1}f^{-1}Z_1| \to |\overline{Z}_{2, 1}| is closed with image containing the dense open |Z_{2, 1}|. After replacing A by its strict henselization (More on Algebra, Lemma 15.123.6) we get the following diagram
where \mathcal{O}_{X_{12}, \overline{y}} \to \mathcal{O} is the map we found in the 5th paragraph of the proof. Since the horizontal composition is finite and flat we can find an extension of valuation rings A'/A and dotted arrow making the diagram commute. After replacing A by A' this means that we obtain a lift g_{12} : \mathop{\mathrm{Spec}}(A) \to X_{12} whose closed point maps into the closure of |p_1^{-1}f^{-1}Z_1|. Then g_1 = p_1 \circ g_{12} : \mathop{\mathrm{Spec}}(A) \to X_1 is a morphism whose closed point maps into the closure of |f^{-1}Z_1|. Since the closure of |f^{-1}Z_1| is disjoint from the closure of |T| and contained in |\overline{Z}_{1, 1}| which is disjoint from |\overline{Z}_{1, 2}| we conclude that g_1 defines a morphism h_1 : \mathop{\mathrm{Spec}}(A) \to W_1 as desired.
Consider a diagram
as in More on Morphisms of Spaces, Lemma 76.40.1. By the previous paragraph for every solid diagram
where \mathop{\mathrm{Im}}(\gamma ) \subset \mathop{\mathrm{Im}}(U_1 \times _ U U_2 \to U) there is an i and an extension h_ i : \mathop{\mathrm{Spec}}(A) \to W_ i of \gamma after possibly replacing A by an extension of valuation rings. Using the valuative criterion of properness for W'_ i \to W_ i, we can then lift h_ i to h'_ i : \mathop{\mathrm{Spec}}(A) \to W'_ i. Hence the dotted arrow in the diagram exists after possibly extending A. Since W is separated over B, we see that the choice of extension isn't needed and the arrow is unique as well, see Morphisms of Spaces, Lemmas 67.41.5 and 67.43.1. Then finally the existence of the dotted arrow implies that W \to B is universally closed by Morphisms of Spaces, Lemma 67.42.5. As W \to B is already of finite type and separated, we win. \square
Lemma 81.14.8. Let S be a scheme. Let X be a Noetherian algebraic space over S. Let U \subset X be a proper dense open subspace. Then there exists an affine scheme V and an étale morphism V \to X such that
the open subspace W = U \cup \mathop{\mathrm{Im}}(V \to X) is strictly larger than U,
(U \subset W, V \to W) is a distinguished square, and
U \times _ W V \to U has dense image.
Proof. Choose a stratification
and morphisms f_ p : V_ p \to U_ p as in Decent Spaces, Lemma 68.8.6. Let p be the smallest integer such that U_ p \not\subset U (this is possible as U \not= X). Choose an affine open V \subset V_ p such that the étale morphism f_ p|_ V : V \to X does not factor through U. Consider the open W = U \cup \mathop{\mathrm{Im}}(V \to X) and the reduced closed subspace Z \subset W with |Z| = |W| \setminus |U|. Then f^{-1}Z \to Z is an isomorphism because we have the corresponding property for the morphism f_ p, see the lemma cited above. Thus (U \subset W, f : V \to W) is a distinguished square. It may not be true that the open I = \mathop{\mathrm{Im}}(U \times _ W V \to U) is dense in U. The algebraic space U' \subset U whose underlying set is |U| \setminus \overline{|I|} is Noetherian and hence we can find a dense open subscheme U'' \subset U', see for example Properties of Spaces, Proposition 66.13.3. Then we can find a dense open affine U''' \subset U'', see Properties, Lemmas 28.5.7 and 28.29.1. After we replace f by V \amalg U''' \to X everything is clear. \square
Theorem 81.14.9.reference Let S be a scheme. Let B be a quasi-compact and quasi-separated algebraic space over S. Let X \to B be a separated, finite type morphism. Then X has a compactification over B.
Proof. We first reduce to the Noetherian case. We strongly urge the reader to skip this paragraph. First, we may replace S by \mathop{\mathrm{Spec}}(\mathbf{Z}). See Spaces, Section 65.16 and Properties of Spaces, Definition 66.3.1. There exists a closed immersion X \to X' with X' \to B of finite presentation and separated. See Limits of Spaces, Proposition 70.11.7. If we find a compactification of X' over B, then taking the scheme theoretic closure of X in this will give a compactification of X over B. Thus we may assume X \to B is separated and of finite presentation. We may write B = \mathop{\mathrm{lim}}\nolimits B_ i as a directed limit of a system of Noetherian algebraic spaces of finite type over \mathop{\mathrm{Spec}}(\mathbf{Z}) with affine transition morphisms. See Limits of Spaces, Proposition 70.8.1. We can choose an i and a morphism X_ i \to B_ i of finite presentation whose base change to B is X \to B, see Limits of Spaces, Lemma 70.7.1. After increasing i we may assume X_ i \to B_ i is separated, see Limits of Spaces, Lemma 70.6.9. If we can find a compactification of X_ i over B_ i, then the base change of this to B will be a compactification of X over B. This reduces us to the case discussed in the next paragraph.
Assume B is of finite type over \mathbf{Z} in addition to being quasi-compact and quasi-separated. Let U \to X be an étale morphism of algebraic spaces such that U has a compactification Y over \mathop{\mathrm{Spec}}(\mathbf{Z}). The morphism
is separated and quasi-finite by Morphisms of Spaces, Lemma 67.27.10 (the displayed morphism factors into an immersion hence is a monomorphism). Hence by Zariski's main theorem (More on Morphisms of Spaces, Lemma 76.34.3) there is an open immersion of U into an algebraic space Y' finite over B \times _{\mathop{\mathrm{Spec}}(\mathbf{Z})} Y. Then Y' \to B is proper as the composition Y' \to B \times _{\mathop{\mathrm{Spec}}(\mathbf{Z})} Y \to B of two proper morphisms (use Morphisms of Spaces, Lemmas 67.45.9, 67.40.4, and 67.40.3). We conclude that U has a compactification over B.
There is a dense open subspace U \subset X which is a scheme. (Properties of Spaces, Proposition 66.13.3). In fact, we may choose U to be an affine scheme (Properties, Lemmas 28.5.7 and 28.29.1). Thus U has a compactification over \mathop{\mathrm{Spec}}(\mathbf{Z}); this is easily shown directly but also follows from the theorem for schemes, see More on Flatness, Theorem 38.33.8. By the previous paragraph U has a compactification over B. By Noetherian induction we can find a maximal dense open subspace U \subset X which has a compactification over B. We will show that the assumption that U \not= X leads to a contradiction. Namely, by Lemma 81.14.8 we can find a strictly larger open U \subset W \subset X and a distinguished square (U \subset W, f : V \to W) with V affine and U \times _ W V dense image in U. Since V is affine, as before it has a compactification over B. Hence Lemma 81.14.7 applies to show that W has a compactification over B which is the desired contradiction. \square
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