Firstly please go with a local Plakias company the tourists are down this year, and any help you can give local companies will be gratefully received,, Harris at Moto Plakias will sort you out a car for collection at the airport ,if it is late at night asmost UK flights are all you have to do is get the orange shuttle bus and a 1min drive to pick up the keys the paperwork will be done the next day at the office in Plakias, avoid Gold Car I had some friends that when they got home were charged over a 1000 euros on there credit card for so called damage to the car, lucky the guy had taken photos time stamped and could prove no such damage occurred it still took them many months to get a refund!
Also be aware that some car hire companies based at the airport close at 10pm again I had some friends coming over to see us and the flight was delayed from 9pm to 11pm when they rang the hire company to explain they would be running late they were told that the office would be closed and it was not possible to collect the car they would have to get a taxi into Chania find a hotel for the night and return the next day to pick up the car, I also rang them to try to arrange a alternative but they simply were not interested in helping and said come back the next day, needless to say I drove to Chania picked up my friends and arranged a car hire with Moto Plakias the next day.
The rates are good but for maybe a few euros more does it relay matter if it saves you a lot of hassle to get a car from someone you can trust.