Asking an employee to sign a bond is illegal. I am not questioning the legality of a stamp paper valued Rs 20, but even if it is of Rs 200, the same will have a value just equal to a paper worth 20 Ps.
Since Bond itself is illegal there is no question of serving the notice period during the bond period. He can submit the resignation now and serve the 3 months notice period and get relieved.
The clause regarding notice period that the the notice required to send an employee out is only 2 months and whereas from an employee side it is 3 months, again is an issue which should be questioned.
Collecting the original certificate of an employee is another illegality in the contract of employment. An employee has every right to decide where he should work. Compelling an employee to work with one employer is against the law.
An employer is bound to issue service certificates to employees when they leave. Though many states are yet to follow the same as a rule, Kerala has moved much ahead in this respect by amending the Kerala Shops and Commercial Establishments Act which provides that no employer should collect the original certificates of his employees, every employer should issue service certificates to his employees, etc.
My advise is that he should submit the resignation with a request to relieve him in 3 months from now and wait for the date. If he is not relieved approach the Labour Officer and simultaneously lodge an FIR against the employer for his act of collecting the certificates. Everything will go smooth then.