Start with a smallish hole right under the step so you can evaluate whether you simply have crushed wood or whether, as it unfortunatly likely, you have water intrusion and the attendent rot. If you want some insight before you do too much tearing up, you may require a surveyor to take moisture content reads traveling out from the step to determine how far the problem may have spread.
In any event, once you get going, you'll need to rip out anything that's got a tinge of rot. You might get lucky and find a damp perimeter of damp but not yet rotten ply where you can stop, buy you'll want to get it well dried before going much further.
I recommend sealing the edges of the existing wood you leave in with CPES or a similar penetrating epoxy sealer. This may be hard to find in UK but you could check in at the WoodenBoat magazine forum (
www.woodenboat.com and then click to forum and ask under repair) where you'll likely find a neighbor - it's a big community - and get a bit of umbridge for having a frozen snot boat but your question is about wood and epoxy.
The exact sequence of the repair depends on how much deck ply you rip out, but you should certainly make the bit right under the step dimensional wood. You may even want to make a beam gunnel to gunnel.
Glass/plywood'glass decks usually involve structural plywood whereas glass/balsa/glass uses the core as a seperating structure, if you see what I mean here. In the former case, any new ply or dimensional wood you put down should have 8:1 beveled edges and land on an identical bevel to give a nice long glue joint that will support people romping about on deck.
You're going to have a major refinishing job no matter what. For the repair, use epoxy to lay your new deck glass to a thickness equal to the original deck - again with the bevel though in this case you'll end up with a bump at the perimeter that will require grinding.
Consider either a creative color scheme that allows finish coating just the repair area, or plan on refinishing the whole deck. There's a huge variety of finishes suitable for this. Seek local advice.
G'luck
Ian