'was alerted' means that he got an alert. That might have been by one of many different ways - it doesn't say. He may have got a warning from another pilot of another plane. There may have been a weather warning. He may have even seen it on a radar. It may have just been his co-pilot that told him. This sentence doesn't say what the disturbance was. Was that mentioned somewhere else? It is similar to 'The captain became aware of the disturbance', but by using 'alerted', the writer is suggesting that someone or something actively informed him, rather than that he just saw it.

The captain = the driver of the plane Was alerted to the disturbance = was notified about the disturbance So someone told the captain that there is a disturbance in the atmosphere.

It means that the captain became aware of the disturbance. Either she or he could have heard the disturbance his/herself or s/he could have been told. It's unspecified how the captain came to know about the disturbance, but the end result is that the captain had knowledge of the disturbance.

機長接收到亂流的警訊