El arma estaba debajo de la mesa.

Because arma is one of those feminine nouns that takes el in the singular when it begins with a stressed a- sound.

So:

• el arma
• el agua
• el aula

This is mainly for pronunciation: la arma is awkward to say.

But the noun is still feminine, which you can see in other places:

• el arma peligrosa = the dangerous weapon
  (peligrosa is feminine)
• las armas = the weapons
  In the plural, it goes back to las

So in your sentence, arma is feminine even though it uses el.

It is feminine.

A good way to tell is by agreement:

• el arma blanca
• el arma escondida
• las armas

If it were masculine, you would expect things like blanco or escondido, but you do not use those here.

So the article looks masculine, but the noun’s gender is still feminine.

Because this sentence is talking about location, and in Spanish location is expressed with estar, not ser.

• estar = to be, in the sense of location/state
• ser = to be, in the sense of identity/essential description

So:

• El arma estaba debajo de la mesa. = The weapon was under the table.
• Era un arma antigua. = It was an old weapon.

You use estar because the sentence tells you where the weapon was.

Estaba is the imperfect, and estuvo is the preterite.

In a sentence like this, estaba is very natural because it describes a background situation or an ongoing state in the past:

• El arma estaba debajo de la mesa.
  = The weapon was under the table.

It simply describes where it was.

Estuvo would sound more like you are viewing that location as a completed, bounded event, for example:

• El arma estuvo debajo de la mesa durante dos horas.
  = The weapon was under the table for two hours.

So if you are just setting the scene or describing a situation, estaba is the usual choice.

Debajo de means under, underneath, or beneath.

So:

• debajo de la mesa = under the table

It is a very common way to express physical position.

You can think of it as a fixed expression:

• debajo de + noun

Examples:

• debajo de la cama = under the bed
• debajo del coche = under the car

Because when debajo is followed by a noun, it normally takes de.

• debajo de la mesa
• debajo del sofá

But debajo can also be used on its own, without a following noun:

• ¿Dónde está? — Debajo.
  = Where is it? — Underneath.

So:

• debajo = underneath
• debajo de + noun = underneath something

That is why the sentence uses debajo de la mesa.

Yes. Bajo la mesa also means under the table.

Both are correct:

• El arma estaba debajo de la mesa.
• El arma estaba bajo la mesa.

In many everyday contexts, debajo de sounds especially common and clear. Bajo is also very normal, but can sometimes sound a bit more concise or slightly more formal depending on context.

For a learner, it is good to know both, but debajo de is extremely useful and very common.

Because Spanish normally uses an article here when referring to a specific table.

• debajo de la mesa = under the table

Without the article, debajo de mesa would sound wrong in normal Spanish.

Spanish often uses articles in places where English might be a bit more flexible, but here the article is definitely needed.

Not necessarily. Arma means weapon in a general sense.

It could refer to:

• a gun
• a knife
• some other weapon

If you want to be specific, Spanish often uses a more precise word:

• pistola = pistol
• revólver = revolver
• rifle = rifle
• cuchillo = knife

So arma is broader than gun.

Yes. Spanish allows some flexibility in word order.

The neutral order here is:

• El arma estaba debajo de la mesa.

But you could also say:

• Debajo de la mesa estaba el arma.

That version puts more emphasis on the location, almost like Under the table was the weapon.

Both are grammatical, but the original sentence is the most straightforward and neutral.