1998 Honda Civic, Check engine light went on,?

Computer read misfire on all 4 cylinders, I noticed a plastic hanging out off valve cover can that be the reason the light went on started running a little rough

Depends on what the plastic is that is hanging off the valve cover.

No, probably not. It could be a lot of different things. When was the last time the distributor cap and rotor were changed? That would affect all four cylinders. Parts cost under $20. Easy to change yourself. When was the last time the fuel filter was changed? That could cause it too. Easy DIY, Parts cost $20-$30. Take care of those first because the car probably needs them anyway. If the problem isn't resolved then come back and we'll go from there.

Misfire on all cylinders isn't going to be caused by a plastic engine cover, but check the spark plugs and wires. If this problem started after a heavy rain, or very spirited car washing, you may wave wet things under the hood that should not get wet. Spray the plug wires sparingly with WD40 and wipe them off with a dry rag. See if the problem goes away. If the valve cover is so loose that its gasket is hanging out- it will leak oil like crazy- there could be too much air infiltrating the PCV system. That's all I can guess for you since I can't see your engine.

Does the car start? No, it could a bad igniter or weak ignition coil or a bad main relay, common on Civics of that vintage. If it runs, check all the plugs and wires, cap and rotor, check for a vacuum leak and check fuel pressure.

All Honda made motors have a common problem with the valves getting tight and they need adjusting every 60,000 miles.
When were the plugs an plug wires changed last?
When was the timing belt replaced?