In general, "closed under operation * on the set $\Sigma$" means that, if you apply operation * (in this case, taking countable intersections) to elements of the set $\Sigma$ (in this case, the set is the $\sigma$-algebra of subsets of a given set $X$), then the result is still an element of $\Sigma$.
Another example which may be more familiar to you: a vector space is closed under addition (addition of vectors is still a vector)
More precisely, in this case, if $\Sigma$ is a $\sigma$-algebra of subsets of $X$, then if $\{A_i\}_{i=1}^\infty \subset \Sigma$, i.e. $A_1, A_2,\dots, A_n, \dots \in \Sigma$ then $\bigcap_{i=1}^\infty A_i = A_1 \cap A_2 \cap \dots \cap A_n \cap \dots \in \Sigma$.
As I said in a comment above, by allowing countable intersections you get finite intersections too. If $A_1,\dots,A_n \in \Sigma$, then because $X\in \Sigma$ too by definition of $\sigma$-algebra, then using the fact $\Sigma$ is closed under countable intersections, $A_1\cap \dots \cap A_n = A_1 \cap \dots \cap A_n \cap X \cap X \cap X \cap \dots \in \Sigma$.
To answer to your addendum:
There seems to be a bit of confusion. If $X=\{x,y,z\}$, then $\mathcal{P}(X)=\{\emptyset,\{x\},\{y\},\{z\},\{x,y\},\{x,z\},\{y,z\},\{x,y,z\}\}$ is the power set of $X$, and a $\sigma$-algebra is a subset of the power set with some additional properties.
So, if $\Sigma=\{\emptyset,\{x\},\{y,z\},\{x,y,z\}\} \subset \mathcal{P}(X)$, then it is a $\sigma$-algebra of subsets of $X$.
To check item 2, what "closed under complementation" means is that, whenever $A\in \Sigma$, we have $A^c=X\setminus A \in \Sigma$. So, we check that for all four elements of $\Sigma$:
$\emptyset \in \Sigma \Rightarrow \{x,y,z\} \in \Sigma$.
$\{x\} \in \Sigma \Rightarrow \{y,z\} \in \Sigma$.
$\{y,z\} \in \Sigma \Rightarrow \{x\} \in \Sigma$.
$\{x,y,z\} \in \Sigma \Rightarrow \emptyset \in \Sigma$.
All these sentences are true, so item 2 is checked.
Also, as a side note, be careful, do not confuse $\emptyset$ with $\{\emptyset\}$.