Lo que can also be followed by the indicative.
You've seen this sentence from the lesson using the subjunctive:
Haré lo que tú quieras si limpias mi habitación.
(I will do whatever you want if you clean my room.)
This sentence could also use the indicative like this:
Haré lo que tú quieres si limpias mi habitación.
(I will do what you want if you clean my room.)
The difference is that in the first one with the subjunctive, the speaker doesn't know what he/she wants. I will do "whatever" you want (whatever that might be...)
In the second sentence using the indicative, we assume that the person has previously said what he/she wants, e.g. watching her favourite film, so then the speaker is saying that he will do what she wants (watching together her favourite film) as long as she cleans his room.
I hope this clarified it.