Assuming you arrive in the domestic terminal and leave from the international one, I would first go over there and try to check in early, just to get that out of the way.
It is always risky to leave the airport and get into suburban traffic when you have to catch another flight, especially an international one.
Your time is limited and I wouldn't spend too much of it in downtown. However even getting there is interesting enough. I would suggest just taking the Blue line from O'Hare to Clark/Lake (1h), then go up and change into the Pink line, this is an elevated train 'The L' that goes around the loop, so you have some views over downtown Chicago. Get off at Washington/Wells and walk back to Clark/Lake (5 blocks) to get back on the Blue line to O'Hare (1h). With only 2.5 hours to spend, this is a very tight schedule.
Photo credit: Peter Hahndorf
To make things worse, the Blue line leaves from near terminal 2, to get there to/from terminal 5 takes at least 15 minutes each.
I would only try this, if you had checked in already, so that when getting back to the airport you would only need to go through security and to the gate, meaning you don't have to be back at 11:30 but maybe at 12:00 or even 12:30.
It would be easier if you could check in through to Tokyo in Boston and don't have to worry about luggage and checkin in O'Hare.
You could also not go downtown, but just look around one of the West Side neighborhoods for a short while. Just take the Blue line to Belmont or Logan Square, spend some time there and then go back. There is nothing too special there, but you can get a feel for Chicago outside of the loop.