This is what it looks like from the top, the hood had been removed from the car.
The second picture was taken through the rear window [zipped open!!] and is looking at the passenger side.
Whatever you do, don't push too hard, or you'll disconnect the tube from the tray. If this happens there's a lot of work involved in dismantling the area behind the seat to get at it.
Try finding the bottom of the drain tube and pushing something up from the bottom,
I find a piece of old flexible net curtain rod is the best, or if you have a Mk 1 with the original aerial, it seems made for the job.
There is a sort of 'flappy thing' at the bottom of the tube, it's designed to keep noise from getting up the tube and into the car, but it can allow bits of debris to get stuck.
Drain holes in the sills
Here's what the drains look like when they are completely removed from the car
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Disclaimer
Any work you do to your car is entirely your own responsibility. If in doubt, you should check technical advice with an independent , qualified person who has seen your car. The MX-5 Owners Club, its officers and forum contributors accept no reponsibility for any damage caused to your person or property as a result of you following or not following the advice offered on this forum.