The following lemma is the basis for our understanding of higher direct images of certain types of sheaves of modules. There are two versions: one for the étale topology and one for the fppf topology.
Lemma 103.5.1. Let \mathcal{M} be a rule which associates to every algebraic stack \mathcal{X} a subcategory \mathcal{M}_\mathcal {X} of \textit{Mod}(\mathcal{X}_{\acute{e}tale}, \mathcal{O}_\mathcal {X}) such that
\mathcal{M}_\mathcal {X} is a weak Serre subcategory of \textit{Mod}(\mathcal{X}_{\acute{e}tale}, \mathcal{O}_\mathcal {X}) (see Homology, Definition 12.10.1) for all algebraic stacks \mathcal{X},
for a smooth morphism of algebraic stacks f : \mathcal{Y} \to \mathcal{X} the functor f^* maps \mathcal{M}_\mathcal {X} into \mathcal{M}_\mathcal {Y},
if f_ i : \mathcal{X}_ i \to \mathcal{X} is a family of smooth morphisms of algebraic stacks with |\mathcal{X}| = \bigcup |f_ i|(|\mathcal{X}_ i|), then an object \mathcal{F} of \textit{Mod}(\mathcal{X}_{\acute{e}tale}, \mathcal{O}_\mathcal {X}) is in \mathcal{M}_\mathcal {X} if and only if f_ i^*\mathcal{F} is in \mathcal{M}_{\mathcal{X}_ i} for all i, and
if f : \mathcal{Y} \to \mathcal{X} is a morphism of algebraic stacks such that \mathcal{X} and \mathcal{Y} are representable by affine schemes, then R^ if_* maps \mathcal{M}_\mathcal {Y} into \mathcal{M}_\mathcal {X}.
Then for any quasi-compact and quasi-separated morphism f : \mathcal{Y} \to \mathcal{X} of algebraic stacks R^ if_* maps \mathcal{M}_\mathcal {Y} into \mathcal{M}_\mathcal {X}. (Higher direct images computed in étale topology.)
Proof.
Let f : \mathcal{Y} \to \mathcal{X} be a quasi-compact and quasi-separated morphism of algebraic stacks and let \mathcal{F} be an object of \mathcal{M}_\mathcal {Y}. Choose a surjective smooth morphism \mathcal{U} \to \mathcal{X} where \mathcal{U} is representable by a scheme. By Sheaves on Stacks, Lemma 96.21.3 taking higher direct images commutes with base change. Assumption (2) shows that the pullback of \mathcal{F} to \mathcal{U} \times _\mathcal {X} \mathcal{Y} is in \mathcal{M}_{\mathcal{U} \times _\mathcal {X} \mathcal{Y}} because the projection \mathcal{U} \times _\mathcal {X} \mathcal{Y} \to \mathcal{Y} is smooth as a base change of a smooth morphism. Hence (3) shows we may replace \mathcal{Y} \to \mathcal{X} by the projection \mathcal{U} \times _\mathcal {X} \mathcal{Y} \to \mathcal{U}. In other words, we may assume that \mathcal{X} is representable by a scheme. Using (3) once more, we see that the question is Zariski local on \mathcal{X}, hence we may assume that \mathcal{X} is representable by an affine scheme. Since f is quasi-compact this implies that also \mathcal{Y} is quasi-compact. Thus we may choose a surjective smooth morphism g : \mathcal{V} \to \mathcal{Y} where \mathcal{V} is representable by an affine scheme.
In this situation we have the spectral sequence
E_2^{p, q} = R^ q(f \circ g_ p)_*g_ p^*\mathcal{F} \Rightarrow R^{p + q}f_*\mathcal{F}
of Sheaves on Stacks, Proposition 96.21.1. Recall that this is a first quadrant spectral sequence hence we may use the last part of Homology, Lemma 12.25.3. Note that the morphisms
g_ p : \mathcal{V}_ p = \mathcal{V} \times _\mathcal {Y} \ldots \times _\mathcal {Y} \mathcal{V} \longrightarrow \mathcal{Y}
are smooth as compositions of base changes of the smooth morphism g. Thus the sheaves g_ p^*\mathcal{F} are in \mathcal{M}_{\mathcal{V}_ p} by (2). Hence it suffices to prove that the higher direct images of objects of \mathcal{M}_{\mathcal{V}_ p} under the morphisms
\mathcal{V}_ p = \mathcal{V} \times _\mathcal {Y} \ldots \times _\mathcal {Y} \mathcal{V} \longrightarrow \mathcal{X}
are in \mathcal{M}_\mathcal {X}. The algebraic stacks \mathcal{V}_ p are quasi-compact and quasi-separated by Morphisms of Stacks, Lemma 101.7.8. Of course each \mathcal{V}_ p is representable by an algebraic space (the diagonal of the algebraic stack \mathcal{Y} is representable by algebraic spaces). This reduces us to the case where \mathcal{Y} is representable by an algebraic space and \mathcal{X} is representable by an affine scheme.
In the situation where \mathcal{Y} is representable by an algebraic space and \mathcal{X} is representable by an affine scheme, we choose anew a surjective smooth morphism \mathcal{V} \to \mathcal{Y} where \mathcal{V} is representable by an affine scheme. Going through the argument above once again we once again reduce to the morphisms \mathcal{V}_ p \to \mathcal{X}. But in the current situation the algebraic stacks \mathcal{V}_ p are representable by quasi-compact and quasi-separated schemes (because the diagonal of an algebraic space is representable by schemes).
Thus we may assume \mathcal{Y} is representable by a scheme and \mathcal{X} is representable by an affine scheme. Choose (again) a surjective smooth morphism \mathcal{V} \to \mathcal{Y} where \mathcal{V} is representable by an affine scheme. In this case all the algebraic stacks \mathcal{V}_ p are representable by separated schemes (because the diagonal of a scheme is separated).
Thus we may assume \mathcal{Y} is representable by a separated scheme and \mathcal{X} is representable by an affine scheme. Choose (yet again) a surjective smooth morphism \mathcal{V} \to \mathcal{Y} where \mathcal{V} is representable by an affine scheme. In this case all the algebraic stacks \mathcal{V}_ p are representable by affine schemes (because the diagonal of a separated scheme is a closed immersion hence affine) and this case is handled by assumption (4). This finishes the proof.
\square
Here is the version for the fppf topology.
Lemma 103.5.2. Let \mathcal{M} be a rule which associates to every algebraic stack \mathcal{X} a subcategory \mathcal{M}_\mathcal {X} of \textit{Mod}(\mathcal{O}_\mathcal {X}) such that
\mathcal{O}_\mathcal {X} is a weak Serre subcategory of \textit{Mod}(\mathcal{O}_\mathcal {X}) for all algebraic stacks \mathcal{X},
for a smooth morphism of algebraic stacks f : \mathcal{Y} \to \mathcal{X} the functor f^* maps \mathcal{M}_\mathcal {X} into \mathcal{M}_\mathcal {Y},
if f_ i : \mathcal{X}_ i \to \mathcal{X} is a family of smooth morphisms of algebraic stacks with |\mathcal{X}| = \bigcup |f_ i|(|\mathcal{X}_ i|), then an object \mathcal{F} of \textit{Mod}(\mathcal{O}_\mathcal {X}) is in \mathcal{M}_\mathcal {X} if and only if f_ i^*\mathcal{F} is in \mathcal{M}_{\mathcal{X}_ i} for all i, and
if f : \mathcal{Y} \to \mathcal{X} is a morphism of algebraic stacks and \mathcal{X} and \mathcal{Y} are representable by affine schemes, then R^ if_* maps \mathcal{M}_\mathcal {Y} into \mathcal{M}_\mathcal {X}.
Then for any quasi-compact and quasi-separated morphism f : \mathcal{Y} \to \mathcal{X} of algebraic stacks R^ if_* maps \mathcal{M}_\mathcal {Y} into \mathcal{M}_\mathcal {X}. (Higher direct images computed in fppf topology.)
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