Learn Spanish (Latin America): No tenemos nada para el espía; no lo pongas en peligro. - We have nothing for the spy; do not put him in danger.

Because this is a negative command! In negative commands (telling someone not to do something), object pronouns like lo always go between the no and the verb. If it were a positive command like "put him," it would attach to the end of the verb: ponlo.

Why does the verb poner change to pongas here?

Pongas is the negative informal command form of poner (to put). To make a negative tú command, you take the present-tense "yo" form (pongo), drop the -o, and add the opposite ending. Since poner is an -er verb, we add -as to get no pongas.

Why does it say no tenemos nada? Isn't that a double negative?

Yes, and double negatives are completely normal and required in Spanish! When a negative word like nada (nothing/anything) comes after the verb, you must also put a no before the verb. Literally, it translates to "We don't have nothing."

Why does espía use the masculine article el if it ends in "-a"?