If you ran the battery totally dry, it's hosed. You need a new one.
Now, I don't know the year of your bike, but a 2012 Ninja 650R can use the YUASA YTX12-BS
A quick check found it for ~$68 on Amazon
Revzilla recommends a slightly different model for the same 2012 650R for about $112, although I've found Amazon often has them cheaper. Don't trust Amazon to tell you if it'll fit correctly, however. They got it wrong for my Triumph but Revzilla and Yausa both agreed on a part number.
I'd put in your specific Year/Model into one of those two websites and order a dry-charged battery. You'll need to get a trickle charger that'll do 0.75A or 1A at most, and it'll probably take an overnight cycle for the initial charge before you can install it.
Amazon says you can get it by Friday:
Yuasa YUAM3RH2S YTX12-BS Battery, Multi-Colored https://www.amazon.com/dp/B000WK4CS4/ref=cm_sw_r_cp_api_glc_fabc_rxo9FbFR46F32