Learn German: Die Affäre ist halt ein großer Skandal. - The affair is simply a big scandal.

Here, halt is not the command for 'stop'. It is a conversational modal particle used to express that something is an obvious, undeniable fact, or to show a bit of resignation (like saying 'that is just the way it is'). In English, it translates best to 'simply' or 'just'.

Could I use the particle eben instead of halt here?

Yes! The particles halt and eben are often completely interchangeable. Both express that a situation is a simple fact that you just have to accept. Saying Die Affäre ist eben ein großer Skandal means exactly the same thing.

Where do I put a modal particle like halt in a sentence?

Modal particles generally sit right in the middle of the sentence. They come after the conjugated verb (here, ist) and any pronouns, but before the most important new information or the end of the sentence (here, ein großer Skandal).

Why does the adjective groß have an -er ending here (großer)?

Skandal is a masculine noun (der Skandal). Because it comes after the verb sein (to be), it is in the nominative case (the basic subject case). After the basic word ein, which doesn't clearly show that the word is masculine, the adjective has to do the work by taking the masculine ending -er.