The Allen-Cahn equation is a semilinear PDE which is deeply linked to the theory of minimal hypersurfaces via a singular limit. We prove curvature estimates and strong sheet separation estimates for stable solutions (building on recent work of Wang-Wei [WW19]) of the Allen-Cahn equation on a 3-manifold. Using these, we are able to show for generic metrics on a 3-manifold, minimal surfaces arising from Allen-Cahn solutions with bounded energy and bounded Morse index are two-sided and occur with multiplicity one and the expected Morse index. This confirms, in the Allen-Cahn setting, a strong form of the multiplicity one conjecture and the index lower bound conjecture of Marques-Neves [Mar14,Nev14] in 3-dimensions regarding min-max constructions of minimal surfaces.Allen-Cahn min-max constructions were recently carried out by Guaraco [Gua18] and Gaspar-Guaraco [GG18]. Our resolution of the multiplicity one and the index lower bound conjectures shows that these constructions can be applied to give a new proof of Yau's conjecture on infinitely many minimal surfaces in a 3-manifold with a generic metric (recently proven by Irie-Marques-Neves [IMN18]) with new geometric conclusions. Namely, we prove that a 3-manifold with a generic metric contains, for every p = 1, 2, 3, . . ., a two-sided embedded minimal surface with Morse index p and area ∼ p OTIS CHODOSH AND CHRISTOS MANTOULIDIS Appendix E. An interpolation lemma 76 References 77Here, h 0 > 0 is a constant that is canonically associated with W (see Section 1.3). A deep result of Hutchinson-Tonegawa [HT00, Theorem 1] ensures that V limits to a varifold with a.e. integer density as ε ց 0. If, in addition, one assumes that the solutions are stable, Tonegawa-Wickramasekera [TW12] have shown that the limiting varifold is stable and satisfies the conditions of Wickramasekera's deep regularity theory [Wic14]; thus the limiting varifold is a smooth stable minimal hypersurface (outside of a codimension 7 singular set). In two dimensions, this was shown by Tonegawa [Ton05].1 Added in proof: There has been dramatic progress in Almgren-Pitts theory since we first posted this article. In particular, we note that A. Song [Son18] has proved the full Yau conjecture in dimensions 3 through 7, and X. Zhou [Zho19] proved the multiplicity one conjecture in the Almgren-Pitts setting, also in dimensions 3 through 7.1.2.3. The multiplicity one-conjecture for limits of the Allen-Cahn equation in 3-manifolds. In their recent work [MN16a], Marques-Neves make the following conjecture:Conjecture 1.5 (Multiplicity one conjecture). For generic metrics on (M n , g), 3 ≤ n ≤ 7, two-sided unstable components of closed minimal hypersurfaces obtained by min-max methods must have multiplicity one.In [MN16a], Marques-Neves confirm this in the case of a one parameter Almgren-Pitts sweepout. The one parameter case had been previously considered for metrics of positive Ricci curvature by Marques-Neves [MN12] and subsequently by Zhou [Zho15]. See also [Gua18, Corollary E] and [GG18, Theorem 1]for results c...