[guided]We want to prove elementarity of $M_i \subseteq M$ for every fixed $i$, so we prove the full satisfaction equivalence for all formulas. The statement we induct on is:
For every formula $\varphi(y_1,\dots,y_m)$, every index $i \in I$, and every tuple $a \in |M_i|^m$,
\begin{align*}
M_i \models \varphi(a)
\quad \Longleftrightarrow \quad
M \models \varphi(a).
\end{align*}
For atomic formulas, no model-theoretic argument is hidden. If a term is evaluated on a tuple from $M_i$, then every function symbol appearing in the term is interpreted in $M$ by the same compatible interpretation used in $M_i$. Thus the value of the term in $M_i$ is the same as its value in $M$. Relation symbols are also interpreted compatibly, so an atomic formula has the same truth value in $M_i$ and in $M$ on tuples from $M_i$.
Negations, conjunctions, disjunctions, and implications are handled by applying the induction hypothesis to the smaller formulas and then using the truth tables for the connectives.
The only substantive case is existential quantification. Let
\begin{align*}
\varphi(y) \equiv \exists x\,\psi(x,y),
\end{align*}
where $y = (y_1,\dots,y_m)$, and fix $i \in I$ and $a \in |M_i|^m$.
First suppose
\begin{align*}
M_i \models \exists x\,\psi(x,a).
\end{align*}
Then there is a witness $c \in |M_i|$ such that
\begin{align*}
M_i \models \psi(c,a).
\end{align*}
The tuple $(c,a)$ lies in $|M_i|^{m+1}$, so the induction hypothesis applied to the smaller formula $\psi$ gives
\begin{align*}
M \models \psi(c,a).
\end{align*}
Therefore the same element $c$ witnesses
\begin{align*}
M \models \exists x\,\psi(x,a).
\end{align*}
Now suppose
\begin{align*}
M \models \exists x\,\psi(x,a).
\end{align*}
Choose a witness $b \in |M|$ with
\begin{align*}
M \models \psi(b,a).
\end{align*}
The element $b$ belongs to some stage $M_j$, because $|M|$ is the union of the underlying sets $|M_j|$. The parameters $a$ already lie in $M_i$. Directedness is used exactly here: choose $k \in I$ such that $i \leq k$ and $j \leq k$. Then both the parameters $a$ and the witness $b$ lie in $M_k$.
Since $(b,a) \in |M_k|^{m+1}$, the induction hypothesis applied to $\psi$ at the stage $k$ gives
\begin{align*}
M_k \models \psi(b,a).
\end{align*}
Thus
\begin{align*}
M_k \models \exists x\,\psi(x,a).
\end{align*}
Because $i \leq k$, the chain hypothesis says that the inclusion $M_i \hookrightarrow M_k$ is elementary. Applying this elementarity to the formula $\exists x\,\psi(x,y)$ with parameter tuple $a \in |M_i|^m$, we obtain
\begin{align*}
M_i \models \exists x\,\psi(x,a).
\end{align*}
This proves the existential case, and hence the induction proves satisfaction equivalence for every first-order formula.[/guided]