Headteacher of Waterloo Road Comprehensive, Jack Rimmer, hires Oxbridge graduate Andrew Treneman, hoping he can improve the school's failing status and bring them back from the bottom of the league tables. Meanwhile, colleagues Tom and Lorna tie the knot - but the groom ends up kissing someone who isn't his new wife.

The aftermath of the car crash affects the entire school. Lorna announces her pregnancy to her new husband, but he isn't so sure he wants a child. And things begin to heat up between Steph and Jack.

A pupil gives birth at the school, but who is the father? Could it be one of the teachers? Lorna terminates her pregnancy behind her husband's back, against Izzie's advice, but Tom changes his mind, and decides he wants the now-aborted baby. Andrew implements a house system with disastrous consequences.

Izzie's ex-husband, Jimmy, causes chaos at the school when he demands access to their children, and Tom confronts Lorna about her apparent miscarriage. Meanwhile, the pupils set up a scam to gain more points in the new house system, but it isn't long before their scheming plot is uncovered. Jack wonders about the sudden improvement in the grades gained by Steph's French class.

Lorna tries out a sexy new image in a bid to catch Tom's attention, while the Head of the English department, Grantly Budgen, suspects one of his students may be taking drugs and approaches Andrew for help. Chlo takes drastic action to convince everyone, including Donte, she was driving on the night of the crash, and Steph stages a break-in to get rid of the suspicious coursework and avoid losing her job, but doesn't do a very good job of it.

An education inspector pays a visit to Waterloo Road, and brings bad news regarding the future of the school. Jack decides the time has come to finally let Steph go, but his task doesn't quite go to plan when she threatens a dire act of vengence, unless he rethinks his actions. Meanwhile, Tom and Izzie struggle to fight their feelings for each other and things come to a head when they find themselves alone.

The staff organise an open day in a bid to impress the inspectors, but events take a turn for the worse, courtesy of Lewis Seddon, when gay pupil Rory starts a petition against homophobic bullying. Holly wakes from her coma and Chlo rushes to her bedside in the hope of finding out what she remembers from the crash. Andrew asks Jack why Steph hasn't been sacked, while Lorna catches Tom and Izzie snogging together.

Tensions run high as the inspectors make their decision about the future of Waterloo Road, while Chlo's nerves are in pieces as she faces her day in court. Kim speaks to the committee about the terrible incident with Lewis Seddon, but they are less than sympathetic to her which causes her to consider quitting her job, much to Andrew's dismay. Lorna continues to remain heartbroken over Tom and Izzie.

At Waterloo Road, a new term is beginning, and things are looking up. The school is launching its first sixth form, and is receiving some promised money from ex-pupil, Roger Aspinall. Izzie and Tom, who are expecting their first child together, get a shock when Lorna returns, who they thought was in Australia.

Jack is mad with Andrew for accepting the acting headteacher role, and lets him do his worst. Back at the Clarkson-Redpath house, Lorna is still staying, and still causing problems. But worse things are to come. Meanwhile, Kim gets a surprise at the school, when an old enemy returns. One with the name of Lewis Seddon...

Izzie finally finds out about Leigh-Ann's hate site about Mika, and is annoyed that she told Kim and Steph before her own mother. Meanwhile, Chlo and Donte have to lie to spend a night together, and Andrew and Lorna share a kiss.

Jack and Andrew learn some interesting secrets about Roger, courtesy of Davina, whilst Brett also confronts his father. Also, Lewis and his girlfriend, Maxine, are still staying at Donte's house.

Outside of Waterloo Road, a pupil is attacked, and this prompts the school to set up a self-defence class. Elesewhere, Lorna goes to the hospital to receive the results of MRI scan, only for her to discover she has multiple sclerosis.

Izzie is trying to recover from the loss of her baby and Tom hasn't come clean about what happened with his pupil, Stacey. Izzie returns to work but after there's another attack in the area she gets very protective of her daughters Chlo and Mika.

Russell Millen, a student teacher, joins the school. Andrew isn't so sure of him after seeing him explode with rage at the pupils, but Kim, as usual, doubts Andrew's views on Russell. Meanwhile, Steph is looking for a home for Maxine. It's seems unlikely that she'll find a place for her to stay, so welcomes Maxine back to her house.

Jack and Kim are mortified when a work placement goes wrong, and Steph speaks up for Maxine with serious consequences. Davina finally lets Jack know how she feels about him.

The interviews for the headmaster’s position at Waterloo Road are taking place, and an ambitious interviewee has Jack going in as the underdog. Meanwhile, Kim tries to find out why Dale is playing truant.

Lorna's struggling to deal with her MS, and when a year group present her with some handmade cards, she gets very emotional and walks out on her class, the school, and her job. Davina, steps in to help in Lorna's absence but Steph doesn't think Davina should be working with kids after her affair with a pupil and tells Jack all about it. Lorna returns and tells everyone that she's leaving Waterloo Road, but wants a weekend away with Izzie first.

In a bid to get the kids eating their five-a-day, Jack launches a healthy eating initiative but when a burger van arrives at the school it threatens to undo all of Jack's good work. Jerry, a wealthy American, has bought Roger Aspinall's business and, therefore, his investment in the new state-of-the-art City Academy. While Jack's just glad they still have a backer Jerry has strong religious beliefs that he's keen to feed into the school. Meanwhile, Andrew Treneman gets offered a permanent job in Rwanda and turns to Kim for advice on whether he should accept the offer or stay at Waterloo Road.

Jed Seddon's burger van is still peddling junk food and drugs to the students and the situation gets worse when pupil Siobhan is rushed to hospital after an overdose. Chlo's sixteenth birthday celebrations turn sour thanks to Lewis who bring drugs to the party and things get even worse when Chlo and Donte announce their engagement which cause Izzie to issue them with an ultimatum. Later Andrew gets annoyed when Jerry uses Lorna's memorial service to preach to the students, and challenges Jerry's beliefs in front of the packed hall.