It is known that given $M\subseteq N$ structure and a substructure such that $M\equiv N$, we do not necessarily have $M\prec N$.
Similarly we can have $M_0\subseteq M_1\subseteq M_2$ such that $M_0\equiv M_1\equiv M_2$ that are not elementary substructure to one another.
Is there a chain where this stops to be true? For example, if I have $\kappa$ that is measurable such that $(M_\mu\mid\mu\in(\kappa\cap Card))$ chain of substructures, all with the same theory $T$ (for convenient sake, let's fix some countable language), and (to have somewhat tame behavior) all are bounded subsets of $\kappa$, does there exists cardinals $\alpha<\beta<\kappa$ such that $M_\alpha\prec M_\beta$ (I would imagine that if 1 such pair exists, there will reflect downwards and we will have at least stationary chain of elementary substructures)?
I played a bit with the problem and I think that the answer is yes. Let $\kappa$ be measurable, and $\mathcal U$ be $\kappa$-complete normal non-principal ultrafilter on $\kappa$, and $j$ be the induced elementary embedding on it's ultrapower.
First let's assume that $|M_\lambda|\ge\lambda$ for $\cal U$-large set $X$, as if $|M_\lambda|<\lambda$ for $\cal U$-large set then it is trivial by normality and the fact that $\kappa$ is a strong limit.
Let $Y=\{\mu\mid \text{there exists $\alpha\in X$ such that }\mu=|M_\mu|\}$ and for $i\in Y$ let $Y_i$ be first model of size $i$, $Y$ satisfy "for all $\mu$ we have $\mu\in Y\iff (\mu\in X\land \mu\text{ is larger than every $X_i$ for $i<\mu$})$". Because $\kappa\in j(X)$, the ultrapower computers the $X_i$ for $i<\kappa$ correctly and the ultrapower thinks $X_{\kappa}\ge\kappa$, then $\kappa\in j(Y)$.
In summery we have $Y\subseteq \kappa$ a $\cal U$-large set such that $(Y_i\mid i\in Y)$ is a chain of elementary equivalent substructures such that $|Y_i|=i$.
My next step was to try to reflect downwards some properties on $Y$ to somehow get a fixed point on "approximate"-Skolem hull operation. Basically fix some Mahlo, or limit of Mahlos, $\nu\in Y$ and look at $(Hull_{Y_{\nu}}(Y_\mu)\mid \mu\in Y\cap\nu)$ and hope it will somehow lend on some $Y_\mu\subseteq Y_\nu$, but I couldn't really find a way to do this.
Does what I wrote can get me somewhere? If it is indeed true, is there some tighter conditions (as my idea was basically to reflect down to $Y$ all of the LCA I want, so it is obviously an overkill if this method indeed works)?
Nothing like this ever holds, even for very simple theories.
Take for example the language consisting of a single binary relation symbol $E$, and the $\{E\}$-theory $T$ that says that $E$ is an equivalence relation with infinitely many classes, all but one of which have exactly two elements and one of which has exactly one element. Given an ordinal $\alpha$, let $\mathcal{M}_\alpha$ be the $\{E\}$-structure with underlying set $$(\alpha\times 2)\cup\{(\alpha,0)\}$$ where $E$ is interpreted as agreement on the left coordinate. Then for all infinite ordinals $\alpha<\beta$ we have $\mathcal{M}_\alpha\subseteq\mathcal{M}_\beta$ and $\mathcal{M}_\alpha\equiv\mathcal{M}_\beta$ (each is a model of $T$, which is complete), but $\mathcal{M}_\alpha\not\preccurlyeq\mathcal{M}_\beta$ (they disagree about which is the "special" $E$-class).
That said, things get much more interesting if we replace "is an elementary substructure of" with "can be elementarily embedded in." Vopenka's principle says that every proper class of structures in the same language contains one that elementarily embeds into another. While these days generally believed to be consistent, VP is a very strong large cardinal axiom; its full strength is not immediately obvious but it is easy to see that it fails assuming the axiom of constructibility.