My (first gen) apple pen won’t connect despite it being in the lighting port

Your Apple Pencil battery may have failed and the Apple Pencil is no longer able to charge up and will not work anymore. If you have access to another pencil that you can try, you can try that and see if it works, or you can set up an appointment to meet with an Apple Genius at a Genius Bar and have them take a look at it. The battery in the pencils are not able to be kept unused for a long period of time and if they get drained below a certain point they will no longer be able to charge and work properly. They can also fail over time as they are batteries and they will suffer from the same thing that all rechargeable batteries suffer from which is why they are considered consumable items. Restarting the iPad isn’t going to help as the issue is going to be with the Pencil itself. It may be giving you the message to turn on your Bluetooth when you plug it in with it turned off because it can see the pencil when it gets the power from the iPad port but as soon as it gets removed the power is removed and it cannot connect to the pencil because the pencil doesn’t power up for the iPad to see it.

These support pages may be helpful with pairing and use of the Pencil with your iPad:

Connect Apple Pencil with your iPad - Apple Support

Charge your Apple Pencil and check the battery - Apple Support

If you continue to experience difficulties, here is one of the better troubleshooting guides:

https://appletoolbox.com/apple-pencil-not-working-heres-our-troubleshooting-guide/

Be aware that if your Pencil has been set-aside for an extended period, unused and uncharged, the Pencil battery may have been damaged through deep discharge. In common with all Li-ion batteries, they must always have some level of charge.

The tiny internal Li-ion battery is susceptible to permanent/irreversible damage through being left discharged for long periods. Even some “new” pencils can exhibit signs of failure out-of-the-box if they are “old stock”. 

It is essential that if you have an Apple Pencil that you charge it regularly - whether used or not - so as to protect the battery from deep-discharge. Do not allow a pencil to remain in low-charge state for any period of time - as the internal battery will fail, rendering the Pencil useless. Setting aside an unused Pencil, for extended periods, is a recipe for premature death of the Pencil battery.

If the Pencil Battery has failed, the only remedy is to replace the Pencil. If the battery has failed and your pencil is within its one-year warranty, you should look to having it replaced by your retailer or at an Apple Store.

Gentle warming of the Pencil (such as placing on a hot water radiator), prior to attempting charging of the Pencil, can sometimes resurrect a dead Pencil battery.