Sara is arrested and put in jail while she waits for her trial. Whilst in the jail firstly she's beaten up by the guards due to her involvement in allowing Michael and co to escape as lots of prison staff lost their jobs. She also encounters Gretchen who's serving time in the same jail. In the male prison the General hears about Sara being arrested and offers £100k to whoever can kill her. Michael goes to see the general and says he will trade his life for hers but the General says that if he killed Michael his pain would last seconds where as by killing Sara Michael would suffer for the rest of his life.
On the outside Michael, Linc and Sucre work on a plan to break Sara out. Mahone is invited into the Bureau and is told the only way he can get his badge back is to join up with Mike and co and relay all the information back to them. Michael finds a blind spot where he can get to Sara but Mahone tells the FBI agent and Michael sets about devising a new plan.
Inside the jail Sara encounters a few problems but she survives. The General puts a bounty on Sara's head for anyone who can kill her and one woman tries but Gretchen saves her - killing the women in the process. Gretchen knows about the break out attempts and wants in. Sara agrees after she saved her.
Michael's new plan is to parachute into the jail to get to Sara who will be waiting at the Chapel and escape through that. Michael writes a letter and makes a recording of himself (much like a terrorist) for Sara and Linc and tells Mahone to give it to them should anything happen to him. He tells Mahone he trusts him.
Linc goes to visit T-bag in the male prison and tells him to set off the fire alarm at 7pm. Lincoln offers him some money (a couple grand I think) which T-bag says is too little. Linc says its all that they have but T-bag has a plan to get the General's 100k he offered for killing Sara. He tricks the General in order to get the name of his contact and tells Lincoln to go and steal the money and wire it to him by 7pm or he wont set off the alarm.
Mahone tells the FBI of Michael's new plan to parachute in and the FBI send more guards to the prison. Sucre and Lincoln go to the General's contacts house and rob him of the money. Sucre rushes off to wire it into T-bags account but fails.
Sara and Gretchen set off a riot and manage to sneak off and make their way to the Chapel to hopefully meet up with Michael.
A plane flies over and someone parachutes out. The agents shoot on sight only to discover that the body is a dummy. We see a flashback of Michael sneaking under the FBI car.
Sara and Gretchen make it to the chapel although Gretchen is wounded from the riot. In the male prison, T-bag discovers the funds have not been wired to him so immediately tells the authorities of Michael's plan. They deploy all their guards to the Chapel.
Two guards find Gretchen at the Chapel entrance but do not see Sara. Gretchen says she's not alone and that God is always with her. Sara manages to get inside the Chapel and his not seen. She meets up with Michael there and they set about escaping out of the other side. The authorities disable all the alarms as T-bag has told them of Michael's plan. This allows them to access the final room and Michael comments that when working with T-bag you always have to remember 'hes a rat'. They get to the door but Michael's plan doesn't work at first. Lincoln, Sucre and Mahone are waiting on the other side but no one is coming out. Eventually Michael says Sara must open the door when he connects the two wires. It becomes clear that Michael will have to die for the door to open and they share a moment in which Michael says he is coming with her making reference to the child Sara is carrying. Michael connects the wires and Sara leaves, meeting up with Linc and co outside. They realise Michael isn't coming out and leave. In the car. Sara opens up the letter and enclosed is a doctors report showing that Michael was indeed dying from a brain tumour. Mahone and Sucre say their goodbyes to the group and leave. At the end Sara and Lincoln are on a boat and view the DVD Michael made for them. He says he was dying anyway as they now know and that he loves them both very much and asks Lincoln to look out for mini Michael and asks Sara to look out for Lincoln as 'he had a tendency to get into trouble'
If you've just read all that I bet you're thinking you should have just watched it
That's from my memory anyway and its very brief